Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/v/vg/vg_1.30.0+ds-1+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/vg-1.30.0+ds-1+b1942ujiws/vg_1.30.0+ds-1+b1_amd64.buildinfo Get source package info: vg=1.30.0+ds-1 Source URL: http://snapshot.notset.fr/mr/package/vg/1.30.0+ds-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 bc=1.07.1-2+b2 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bison=2:3.7.5+dfsg-1 bsdextrautils=2.36.1-7 bsdmainutils=12.1.7+nmu2 bsdutils=1:2.36.1-7 build-essential=12.9 bwa=0.7.17-6 bzip2=1.0.8-4 ca-certificates=20210119 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.75 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 docbook=4.5-6 docbook-to-man=1:2.0.0-45 docbook-xml=4.5-9 docbook-xsl=1.79.2+dfsg-1 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 elfutils=0.183-3 fastahack=1.0.0+dfsg-7 file=1:5.39-3 findutils=4.8.0-1 flex=2.6.4-8 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gawk=1:5.1.0-1 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gtk-doc-tools=1.33.2-1 gzip=1.10-4 help2man=1.48.2 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 jq=1.6-2.1 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=10.2.1-6 libasm1=0.183-3 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbackward-cpp-dev=1.5-2 libbinutils=2.35.2-2 libblas3=3.9.0-3 libblkid-dev=2.36.1-7 libblkid1=2.36.1-7 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-8 libboost-program-options1.74.0=1.74.0-8 libboost1.74-dev=1.74.0-8 libbrotli-dev=1.0.9-2+b2 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.1 libcurl4=7.74.0-1.1 libcurl4-gnutls-dev=7.74.0-1.1 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.4 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdisorder-dev=0.0.2+git20130809.8062ee1-2 libdisorder0=0.0.2+git20130809.8062ee1-2 libdivsufsort-dev=2.0.1-5 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.7.1 libdw-dev=0.183-3 libdw1=0.183-3 libelf-dev=0.183-3 libelf1=0.183-3 libexpat1=2.2.10-2 libexpat1-dev=2.2.10-2 libfastahack-dev=1.0.0+dfsg-7 libfastahack0=1.0.0+dfsg-7 libffi-dev=3.3-6 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.11.0-1 libfml-dev=0.1+git20190320.b499514-1+b1 libfml0=0.1+git20190320.b499514-1+b1 libfontconfig-dev=2.13.1-4.2 libfontconfig1=2.13.1-4.2 libfontconfig1-dev=2.13.1-4.2 libfreetype-dev=2.10.4+dfsg-1 libfreetype6=2.10.4+dfsg-1 libfreetype6-dev=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libglib2.0-0=2.66.7-2 libglib2.0-bin=2.66.7-2 libglib2.0-data=2.66.7-2 libglib2.0-dev=2.66.7-2 libglib2.0-dev-bin=2.66.7-2 libgmp-dev=2:6.2.1+dfsg-1 libgmp10=2:6.2.1+dfsg-1 libgmpxx4ldbl=2:6.2.1+dfsg-1 libgnutls30=3.7.1-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.7.4-1 libhogweed6=3.7-2.1 libhts-dev=1.11-4 libhts3=1.11-4 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjansson-dev=2.13.1-1.1 libjansson4=2.13.1-1.1 libjbig0=2.1-3.1+b2 libjemalloc-dev=5.2.1-2 libjemalloc2=5.2.1-2 libjpeg62-turbo=1:2.0.6-2 libjq1=1.6-2.1 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-2 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblz4-dev=1.9.3-1 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 liblzo2-2=2.10-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmhash2=0.9.9.9-9 libmount-dev=2.36.1-7 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses5-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2.1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libonig5=6.9.6-1.1 libosp5=1.5.2-13+b2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.36-2 libpcre2-32-0=10.36-2 libpcre2-8-0=10.36-2 libpcre2-dev=10.36-2 libpcre2-posix2=10.36-2 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-4 libprotobuf-dev=3.12.4-1 libprotobuf-lite23=3.12.4-1 libprotobuf23=3.12.4-1 libprotoc-dev=3.12.4-1 libprotoc23=3.12.4-1 libpsl5=0.21.0-1.2 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.2-2 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libraptor2-0=2.0.14-1.2 libraptor2-dev=2.0.14-1.2 librasqal3=0.9.33-0.1 librasqal3-dev=0.9.33-0.1 librdf0=1.0.17-1.1+b1 librdf0-dev=1.0.17-1.1+b1 libreadline8=8.1-1 librhash0=1.4.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libselinux1-dev=3.1-3 libsepol1=3.1-1 libsepol1-dev=3.1-1 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-7 libsmithwaterman-dev=0.0+git20160702.2610e25-11 libsmithwaterman0=0.0+git20160702.2610e25-11 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.34.1-3 libssh2-1=1.9.0-2 libssl1.1=1.1.1j-1 libssw-dev=1.1-13 libssw0=1.1-13 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-2 libtabixpp-dev=1.1.0-4 libtabixpp0=1.1.0-4 libtasn1-6=4.16.0-2 libtcl8.6=8.6.11+dfsg-1 libthai-data=0.1.28-4 libthai0=0.1.28-4 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtk8.6=8.6.11-2 libtool=2.4.6-15 libtsan0=10.2.1-6 libtsl-hopscotch-map-dev=2.3.0-1 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-2 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libvcflib-dev=1.0.2+dfsg-2 libvcflib-tools=1.0.2+dfsg-2 libvcflib1=1.0.2+dfsg-2 libwebp6=0.6.1-2+b1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-dev=2:1.7.0-2 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-render0-dev=1.14-3 libxcb-shm0=1.14-3 libxcb-shm0-dev=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1.1 libxext6=2:1.3.3-1.1 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.3+b1 libxml2-dev=2.9.10+dfsg-6.3+b1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxslt1-dev=1.1.34-4 libxslt1.1=1.1.34-4 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libyajl-dev=2.1.0-3 libyajl2=2.1.0-3 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.19-1 littler=0.3.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncal=12.1.7+nmu2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 opensp=1.5.2-13+b2 openssl=1.1.1j-1 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-4 protobuf-compiler=3.12.4-1 pv=1.6.6-1+b1 python3=3.9.2-2 python3-distutils=3.9.2-1 python3-lib2to3=3.9.2-1 python3-lxml=4.6.2-1 python3-minimal=3.9.2-2 python3-pkg-resources=52.0.0-3 python3-pygments=2.7.1+dfsg-1 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 r-base-core=4.0.4-1 r-cran-assertthat=0.2.1-2 r-cran-brio=1.1.1-1 r-cran-callr=3.5.1-1 r-cran-cli=2.3.0-1 r-cran-colorspace=2.0-0+dfsg-1 r-cran-crayon=1.4.0-1 r-cran-desc=1.2.0-3 r-cran-diffobj=0.3.2-1 r-cran-digest=0.6.27-1 r-cran-ellipsis=0.3.1-1 r-cran-evaluate=0.14-2 r-cran-fansi=0.4.2-1 r-cran-farver=2.0.3-1+b1 r-cran-ggplot2=3.3.3+dfsg-1 r-cran-glue=1.4.2-1 r-cran-gridbase=0.4-7-5 r-cran-gtable=0.3.0+dfsg-2 r-cran-isoband=0.2.3-2 r-cran-jsonlite=1.7.2+dfsg-1 r-cran-labeling=0.4.2-1 r-cran-lattice=0.20-41-1+b1 r-cran-lifecycle=0.2.0-2 r-cran-littler=0.3.12-1 r-cran-magrittr=2.0.1-1 r-cran-mass=7.3-53.1-1 r-cran-matrix=1.3-2-1 r-cran-mgcv=1.8-34-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.152-1 r-cran-pillar=1.4.7-1 r-cran-pkgbuild=1.2.0-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.1-1 r-cran-pkgload=1.1.0-1 r-cran-plyr=1.8.6-2 r-cran-praise=1.0.0-4 r-cran-prettyunits=1.1.1-2 r-cran-processx=3.4.5-1 r-cran-ps=1.5.0-1 r-cran-r6=2.5.0-1 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.6-1 r-cran-rematch2=2.1.2-2 r-cran-rlang=0.4.10-1 r-cran-rprojroot=2.0.2-1 r-cran-rstudioapi=0.13-1 r-cran-scales=1.1.1-1 r-cran-testthat=3.0.1-1 r-cran-tibble=3.0.6+dfsg-1 r-cran-utf8=1.1.4-2 r-cran-vctrs=0.3.6-1 r-cran-viridislite=0.3.0-4 r-cran-waldo=0.2.3-2 r-cran-withr=2.4.1-1 rapidjson-dev=1.1.0+dfsg2-7 raptor2-utils=2.0.14-1.2 rasqal-utils=0.9.33-0.1 readline-common=8.1-1 rs=20200313-1 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sgml-data=2.0.11+nmu1 sysvinit-utils=2.96-6 tabix=1.11-4 tar=1.34+dfsg-1 tzdata=2021a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.36.1-7 uuid-dev=2.36.1-7 x11-common=1:7.7+22 x11proto-dev=2020.1-1 x11proto-xext-dev=2020.1-1 xdg-utils=1.1.3-4 xml-core=0.18+nmu1 xorg-sgml-doctools=1:1.11-1.1 xsltproc=1.1.34-4 xtrans-dev=1.4.0-1 xxd=2:8.2.2434-3 xz-utils=5.2.5-2 zip=3.0-12 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-OlWF3C && dpkg-source --no-check -x /*.dsc /build/vg-OlWF3C/vg-1.30.0+ds && cd /build/vg-OlWF3C/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 11 Mar 2021 23:18:13 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-OlWF3C" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-OlWF3C/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504693" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/vg-OlWF3C /tmp/vg-1.30.0+ds-1+b1942ujiws bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.qHx75qFUFT as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.qHx75qFUFT Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (722 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.qHx75qFUFT Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1146 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.qHx75qFUFT I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d vg=1.30.0+ds-1 && mkdir -p /build/vg-OlWF3C && dpkg-source --no-check -x /*.dsc /build/vg-OlWF3C/vg-1.30.0+ds && cd /build/vg-OlWF3C/vg-1.30.0+ds && { printf '%s' 'vg (1.30.0+ds-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 11 Mar 2021 23:18:13 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/vg-OlWF3C"' exec /tmp/mmdebstrap.qHx75qFUFT Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 95.1 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (dsc) [2979 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (tar) [95.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main vg 1.30.0+ds-1 (diff) [114 kB] Fetched 95.1 MB in 1min 17s (1234 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'vg_1.30.0+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting vg in /build/vg-OlWF3C/vg-1.30.0+ds dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-10 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 dpkg-source: info: applying fix-handlegraph I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-OlWF3C/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504693" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.qHx75qFUFT dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.30.0+ds-1+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' find /build/vg-OlWF3C/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j4 clean make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean rm -rf ../bin ../lib make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_autoreconf --sourcedirectory=/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/help mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j4 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done -- Detecting C compiler ABI info - done gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_objs make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' rm -f lib/libboost_* rm -Rf include/boost touch lib/cleaned_old_boost g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 cp deps/BBHash/BooPHF.h /build/vg-OlWF3C/vg-1.30.0+ds/include [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cp -r deps/sparsepp/sparsepp include/ rm -Rf include/dynamic.hpp include/dynamic # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make -- Setting build type to 'Debug' as none was specified. [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ -- Detecting C compiler ABI info - done . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/vg-OlWF3C/vg-1.30.0+ds/include/ -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done cp ./deps/gfakluge/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/ -- Detecting CXX compiler ABI info cd ./deps/lru_cache && cp *.h* /build/vg-OlWF3C/vg-1.30.0+ds/include/ cp deps/sha1/*.h* /build/vg-OlWF3C/vg-1.30.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include cp -r deps/dozeu/simde include [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Building in Debug mode -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake --color= Scanning dependencies of target cw-bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 7%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/cw-bwt.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake --color= [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp Scanning dependencies of target rle_bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 14%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_bwt.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' diff: include/vg_environment_version.hpp: No such file or directory make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake --color= Scanning dependencies of target h0_lz77 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 21%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 [ 28%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/h0_lz77.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -o cw-bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 28%] Built target cw-bwt make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 35%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/benchmark.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 42%] Built target rle_bwt make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake --color= [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o Scanning dependencies of target rle_lz77_v2 cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 50%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp [ 57%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 57%] Built target benchmark make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 64%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp [ 71%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 71%] Built target h0_lz77 make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake --color= Scanning dependencies of target debug make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 78%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/internal -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/debug.dir/debug.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/debug.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 85%] Built target debug [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 92%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [ 92%] Built target rle_lz77_v2 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' [100%] Built target rle_lz77_v1 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/vg-OlWF3C/vg-1.30.0+ds/deps/DYNAMIC/include/* include/dynamic g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp ln -s `which shuf` bin/shuf . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I .//../sonLib/lib/ -c impl/*.c . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp configure.ac:15: installing './compile' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h yes rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info yes checking for C++ compiler default output file name... a.out checking for suffix of executables... -- Detecting CXX compiler ABI info - done mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/dozeu && cp deps/dozeu/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/dozeu/ checking whether we are cross compiling... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' none needed checking whether gcc understands -c and -o together... -- Found htslib, version 1.11-4 yes checking dependency style of gcc... -- Checking for module 'jansson' -- Found jansson, version 2.13.1 gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... -- Configuring done BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee 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In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix [ 2%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp ok /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir checking for sysroot... no checking for a working dd... cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= [ 7%] No download step for 'handlegraph' Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". /usr/bin/cmake -E echo_append /bin/dd checking how to truncate binary pipes... Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /bin/dd bs=4096 count=1 [ 9%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 11%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update checking for mt... no checking if : is a manifest tool... [ 14%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append no checking how to run the C preprocessor... /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 16%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake gcc -E cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o checking for ANSI C header files... -- The C compiler identification is GNU 10.2.1 /usr/bin/ranlib libsdsl.a -- The CXX compiler identification is GNU 10.2.1 yes -- Detecting C compiler ABI info checking for sys/types.h... yes make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' checking for sys/stat.h... [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 yes checking for stdlib.h... /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all yes make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend checking for string.h... make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= -- Detecting C compiler ABI info - done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info yes make -f CMakeFiles/Makefile2 preinstall checking for memory.h... make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: 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Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp yes -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp checking for strings.h... -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a yes checking for inttypes.h... -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure yes [ 19%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 checking for stdint.h... make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks [ 21%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= yes Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Scanning dependencies of target handlegraph_objs make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' checking for unistd.h... [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Scanning dependencies of target handlegraph_static make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Scanning dependencies of target handlegraph_shared make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 23%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' checking for exit in -lboost_program_options... [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 26%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... [ 26%] Built target handlegraph [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". 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Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 30%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 42%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp mv -f .deps/vw-main.Tpo .deps/vw-main.Po depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 52%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o [ 59%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 61%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp [ 66%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 69%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 76%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 76%] Built target vgio_static /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson -lhandlegraph -ldl In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem 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-Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest 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-isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem 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-I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack 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-f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem 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.libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx2 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o bin/vg-avx2 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j4 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c libhandlegraph is root project or external_project -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Looking for C++ include cstdio - found ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' rm -f lib/libboost_* rm -Rf include/boost touch lib/cleaned_old_boost rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I .//../sonLib/lib/ -c impl/*.c In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 10.2.1 [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake -- Detecting CXX compiler ABI info cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". 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Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". 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Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc configure.ac:15: installing './compile' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp yes checking that generated files are newer than configure... done configure: creating ./config.status In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 59%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 61%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp [ 66%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ 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/usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand 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-isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mavx -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o bin/vg-avx obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j4 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c libhandlegraph is root project or external_project -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp rm -f lib/libboost_* rm -Rf include/boost touch lib/cleaned_old_boost [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake 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Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". 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Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments -- Configuring done configure.ac:15: installing './compile' configure.ac:3: installing './missing' -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= cluster/Makefile.am: installing './depcomp' make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= yes (GNU style) checking dependency style of g++... Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' gcc3 checking how to run the C++ preprocessor... [ 26%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... 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[ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp yes checking that generated files are newer than configure... done configure: creating ./config.status In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o config.status: executing libtool commands /usr/bin/ranlib libsdsl.a . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' yes checking whether make supports nested variables... yes [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' checking whether the C++ compiler works... Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- 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The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status [ 30%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged [ 35%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 40%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp [ 42%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 45%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo [ 47%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o [ 50%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 54%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 59%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 66%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 [ 71%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 78%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 80%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 [ 85%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp [ 88%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 90%] Built target vgio . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 95%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o [ 97%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse4.1 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o bin/vg-sse4.1 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j4 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c libhandlegraph is root project or external_project -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o -- Detecting CXX compiler ABI info - done mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Performing Test HAVE_CXA_DEMANGLE - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Configuring done [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp ar rvs lib/libgssw.a obj/gssw.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' rm -f lib/libboost_* rm -Rf include/boost touch lib/cleaned_old_boost [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") configure.ac:15: installing './compile' -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= [100%] Linking CXX static library libsdsl.a Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake Scanning dependencies of target link_target Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg [ 2%] Creating directories for 'handlegraph' make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 [ 2%] Built target link_target /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix [ 4%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= [ 7%] No download step for 'handlegraph' Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". /usr/bin/cmake -E echo_append Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/ranlib libsdsl.a [ 9%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc [ 11%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update [ 14%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes [ 16%] Performing configure step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph checking for a thread-safe mkdir -p... Re-run cmake no build system arguments /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... -- Configuring done yes -- Generating done checking whether make supports nested variables... -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure yes make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 19%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks checking whether the C++ compiler works... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make -f CMakeFiles/Makefile2 preinstall yes checking for C++ compiler default output file name... a.out checking for suffix of executables... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a [ 21%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 checking whether we are cross compiling... /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= no checking for suffix of object files... make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' o checking whether we are using the GNU C++ compiler... /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' yes checking whether g++ accepts -g... Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... [ 23%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 23%] Built target handlegraph make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend gcc3 checking how to run the C++ preprocessor... make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' g++ -E [ 26%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status [ 28%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 33%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o [ 38%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 50%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp [ 57%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 59%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o [ 66%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 69%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 71%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 78%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 80%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp [ 83%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp [ 85%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 90%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o [ 92%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 95%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 97%] Built target vgio depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio_static make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f lib/libxg.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -mssse3 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o bin/vg-ssse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' rm -f build_gcsa convert_graph gcsa_format try_extend algorithms.o build_gcsa.o convert_graph.o dbg.o files.o gcsa.o gcsa_format.o internal.o lcp.o path_graph.o support.o try_extend.o utils.o libgcsa2.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/lib' and '/nonexistent/include' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target uninstall-sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp" -- 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"/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp" -- Uninstalling 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"/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp" -- Uninstalling "/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp" make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd gfakluge && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' rm -f gfak rm -f src/*.o rm -f *.a rm -f x.sort rm -f y.sort rm -rf bin rm -rf build rm -f test_test.gfa rm -f q_test.gfa make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gfakluge' cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' cd ./deps && cd vowpal_wabbit && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_shared.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -P CMakeFiles/handlegraph_objs.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd ./deps && cd libvgio && make clean make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make -j4 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /build/vg-OlWF3C/vg-1.30.0+ds/include Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/gssw && make && cp lib/* /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp obj/* /build/vg-OlWF3C/vg-1.30.0+ds/obj && cp src/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c libhandlegraph is root project or external_project -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) gcc -std=c99 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Configuring done [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend In file included from /usr/include/string.h:495, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/vg-OlWF3C/vg-1.30.0+ds/include" make libs && cp lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS && cp src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin/* /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sonLib' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ && cp -r src/include/structures /build/vg-OlWF3C/vg-1.30.0+ds/include/ make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/vg-OlWF3C/vg-1.30.0+ds/include -L. -L/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ar rc /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sublinear-Li-Stephens' rm -f lib/libboost_* rm -Rf include/boost touch lib/cleaned_old_boost rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libhandlegraph' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /build/vg-OlWF3C/vg-1.30.0+ds/obj make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp g++ -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[2]: 'bin/shuf' is up to date. [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp g++ -Wl,-z,relro -Wl,-z,now -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/progress_bar' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/vg-OlWF3C/vg-1.30.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib && cp lib/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/vg-OlWF3C/vg-1.30.0+ds/include -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvw.* /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && rm -Rf vowpalwabbit/*.la vowpalwabbit/.libs . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./autogen.sh || true ./autogen.sh: 22: [[: not found ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ rm -f /build/vg-OlWF3C/vg-1.30.0+ds/include/vg.pb.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_LIBRARY_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/lib -DCMAKE_INSTALL_PREFIX=/build/vg-OlWF3C/vg-1.30.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.4 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.4 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.12.4") Protobuf will be /usr/lib/x86_64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/x86_64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/clean make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/handlegraph.dir/cmake_clean.cmake make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks /usr/bin/ranlib libsdsl.a make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". Scanning dependencies of target handlegraph make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/tmp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append make -f CMakeFiles/Makefile2 all /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update make -f CMakeFiles/Makefile2 preinstall [ 9%] No patch step for 'handlegraph' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E echo_append Install the project... /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp [ 11%] Performing configure step for 'handlegraph' -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp cd 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/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp Re-run cmake no build system arguments -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 14%] Performing build step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/pinchesAndCacti' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/vg.proto cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ configure.ac:15: installing './compile' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0 (100000)... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dbg.cpp config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" ./configure --with-boost=no --with-boost-program-options=boost_program_options"" /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking whether the Boost::Program_Options library is available... yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp yes checking that generated files are newer than configure... done configure: creating ./config.status /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && make clean && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16" LDFLAGS="-L/build/vg-OlWF3C/vg-1.30.0+ds/lib" make make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making clean in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' rm -f vw active_interactor test -z "liballreduce.la libvw.la " || rm -f liballreduce.la libvw.la rm -f ./so_locations rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making clean in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' rm -f spanning_tree rm -rf .libs _libs rm -f *.o rm -f ../vowpalwabbit/*.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making clean in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' rm -f library_example ezexample_train ezexample_predict rm -rf .libs _libs rm -f *.o rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' rm -rf .libs _libs rm -f *.lo make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gcsa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest 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io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c lcp.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_graph.cpp depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 59%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 61%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg.pb.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:28, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_emitter.cpp In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 66%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/alignment_io.cpp depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:8: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/vg/vg.pb.h:23, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/edit.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/hfile_cppstream.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/json2pb.cpp [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_emitter.cpp [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/registry.cpp depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/stream_multiplexer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/deps/libhandlegraph/src/include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/src/vpkg.cpp [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -Wl,-rpath,/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson handlegraph-prefix/lib/libhandlegraph.so -ldl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so -- Set runtime path of "/build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.so" to "" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include -- Up-to-date: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/edit.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/json2pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/loader.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/registry.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/io/stream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libvgio' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic 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.libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -pthread -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o active_interactor active_interactor.o -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o active_interactor active_interactor.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lboost_program_options -L/lib -lz -lpthread -pthread In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -L/build/vg-OlWF3C/vg-1.30.0+ds/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L. -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -O3 -msse3 -pthread -pthread -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o vw vw-main.o libvw.la liballreduce.la -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/vw vw-main.o -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ./.libs/libvw.so ./.libs/liballreduce.so -lboost_program_options -L/lib -lz -lpthread -pthread make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/library_example library_example.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_train ezexample_train.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -o .libs/ezexample_predict ezexample_predict.o -lboost_program_options -L/lib -lz -lpthread -L/build/vg-OlWF3C/vg-1.30.0+ds/lib ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so -pthread make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /build/vg-OlWF3C/vg-1.30.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /build/vg-OlWF3C/vg-1.30.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' CXXFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" CFLAGS="-g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf make -j4 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf make[2]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/vg-OlWF3C/vg-1.30.0+ds Library will be installed in '/build/vg-OlWF3C/vg-1.30.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[2]: 'bin/shuf' is up to date. -- The CXX compiler identification is GNU 10.2.1 -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done -- Build files have been written to: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [100%] Linking CXX static library libsdsl.a cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/*' rm -f '/build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite -B/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' cd /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/vg-OlWF3C/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/include'. The library files are located in '/build/vg-OlWF3C/vg-1.30.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /build/vg-OlWF3C/vg-1.30.0+ds/lib . ./source_me.sh && rm -Rf /build/vg-OlWF3C/vg-1.30.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/vg-OlWF3C/vg-1.30.0+ds/include:/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/vg-OlWF3C/vg-1.30.0+ds/lib && cp -r bdsg/include/* /build/vg-OlWF3C/vg-1.30.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/vg-OlWF3C/vg-1.30.0+ds/include make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' rm -r bdsg/obj make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o rm -r lib rm -r bin make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gcsa2' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c bwtmerge.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/node.cpp -o bdsg/obj/node.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/odgi.cpp -o bdsg/obj/odgi.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c dynamic_gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_structs.cpp -o bdsg/obj/packed_structs.o In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c files.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/files.h:29, from files.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c internal.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c test.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/test.h:28, from test.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c variants.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c build_ri.cpp rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/node.o bdsg/obj/odgi.o bdsg/obj/packed_graph.o bdsg/obj/packed_structs.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c merge_gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c metadata_tool.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c remove_seq.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_ri build_ri.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o benchmark benchmark.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/vg-OlWF3C/vg-1.30.0+ds/include -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/vg-OlWF3C/vg-1.30.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /build/vg-OlWF3C/vg-1.30.0+ds/lib make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c path_cover.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c utils.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -c gfa2gbwt.cpp In file included from /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp:8, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/utils.h:35, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/support.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/algorithms.h:31, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/gbwt.h:29, from /build/vg-OlWF3C/vg-1.30.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /build/vg-OlWF3C/vg-1.30.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/vg-OlWF3C/vg-1.30.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/build/vg-OlWF3C/vg-1.30.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 make[3]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:103:53: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:49, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /build/vg-OlWF3C/vg-1.30.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_manager.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/build/vg-OlWF3C/vg-1.30.0+ds/include -isystem /build/vg-OlWF3C/vg-1.30.0+ds/include -I. -I/build/vg-OlWF3C/vg-1.30.0+ds/src -I/build/vg-OlWF3C/vg-1.30.0+ds/src/unittest -I/build/vg-OlWF3C/vg-1.30.0+ds/src/subcommand -I/build/vg-OlWF3C/vg-1.30.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -ffile-prefix-map=/build/vg-OlWF3C/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg-plain obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/driver.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gapless_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/min_distance.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/seed_clusterer.o obj/unittest/sequence_complexity.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/srpe_filter.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/recalibrate_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/srpe_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o -lvg -L/build/vg-OlWF3C/vg-1.30.0+ds/lib /build/vg-OlWF3C/vg-1.30.0+ds/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -ljemalloc -Wl,-Bstatic -lhts -ldeflate -lz -llzma -lprotobuf -lz -Wl,-Bdynamic -lpthread -lm -lbz2 make[2]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' cp bin/vg-plain debian/help/vg PATH=$PATH:/build/vg-OlWF3C/vg-1.30.0+ds/debian/help \ help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/vg-OlWF3C/vg-1.30.0+ds' cp -v /build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-* /build/vg-OlWF3C/vg-1.30.0+ds/debian/help/ '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-avx' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx' '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-avx2' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx2' '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-plain' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-plain' '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-sse3' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-sse3' '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-sse4.1' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-sse4.1' '/build/vg-OlWF3C/vg-1.30.0+ds/bin/vg-ssse3' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-ssse3' set +e \ ; export PATH="$PATH:/build/vg-OlWF3C/vg-1.30.0+ds/debian/help" \ ; for BIN in /build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-* \ ; do echo "Testing ${BIN}" \ && cp -v "${BIN}" "/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg" \ && . /build/vg-OlWF3C/vg-1.30.0+ds/source_me.sh \ && ( cd /build/vg-OlWF3C/vg-1.30.0+ds/test && prove -v t/ ) \ ; if [ $? != 0 ] \ && [ "${BIN}" = "/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-plain" ] \ ; then exit 255 \ ; fi \ ; done \ ; set -e Testing /build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg' ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TL1bGk/stacktrace.txt Please include the stack trace file in your bug report! t/00_unittest.t ....... 1..1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vg test is a Catch v1.8.2 host application. Run with -? for options ------------------------------------------------------------------------------- We can convert a two-tailed graph to Cactus ------------------------------------------------------------------------------- src/unittest/cactus.cpp:16 ............................................................................... src/unittest/cactus.cpp:16: FAILED: due to a fatal error condition: SIGILL - Illegal instruction signal =============================================================================== test cases: 45 | 44 passed | 1 failed assertions: 7396 | 7395 passed | 1 failed not ok 1 - vg unit tests complete successfully # got: '132' # expected: '0' Failed 1/1 subtests t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YVUpQT/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error:[vg::Constructor] non-ATGCN characters found in variant: x 973 . G A,* 99 . AC=2;LEN=1;NA=2;NS=1;TYPE=snp index file tiny/ambiguous.fa.fai not found, generating... warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. t/02_vg_construct.t ... 1..28 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges ok 7 - node size is manageable by default ok 8 - construction of a very complex region succeeds ok 9 - the complex graph has the expected number of nodes ok 10 - the complex graph has the expected number of edges ok 11 - the ordering of variants at the same position has no effect on the resulting graph ok 12 - construction does not fail when the first position in the VCF is repeated and has an indel ok 13 - the size of the regions used in construction has no effect on the graph ok 14 - the number of threads used in construction has no effect on the graph ok 15 - the number of threads and regions used in construction has no effect on the graph ok 16 - construction of a graph with two head nodes succeeds ok 17 - the graph contains all the sequence in the reference and VCF ok 18 - varying the max node size does not affect graph length ok 19 - nodes are correctly capped in size ok 20 - -R --region flag is respected ok 21 - vg construct does not require a vcf ok 22 - vg construct respects node size limit ok 23 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 24 - vg constructs the correct graph for inversions not ok 25 - vg construct skips variants with . ALTs # got: '' # expected: '1' ok 26 - VCF with * alleles is rejected ok 27 - Reference with ambiguity codes has them coerced to Ns ok 28 - Expected number of Ns are created Failed 1/28 subtests t/03_vg_view.t ........ 1..19 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM ok 5 - view can round-trip JSON and GAM ok 6 - view can reconstruct a VG graph from JSON ok 7 - view can pass through VG when loading as vg::VG ok 8 - view can pass through semantically identical VG normally ok 9 - view parses sample names ok 10 - view can handle fastq input ok 11 - view can translate graphs with 2-node cycles ok 12 - view outputs properly oriented GFA ok 13 - view produces the expected number of lines of dot output from a cyclic graph ok 14 - streaming JSON output produces the expected number of chunks ok 15 - duplicate warnings can be suppressed when loading as vg::VG ok 16 - gfa graphs with overlaps are rejected ok 17 - GFA import produces a concise error message when overlaps are present ok 18 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 19 - GFA import produces a concise error message in that case ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tQ6KmH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fbHM4v/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9NVvK2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zwMIQE/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JgDHTe/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vFtHDM/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xozLis/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_s0ITL2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZfdbCH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Fbihvm/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BzVz41/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4IB9EF/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_AZiPQd/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7CHUwE/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_QNuiyw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OWF7ge/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_87Qq8D/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VNY932/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_H6ENst/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rFes6Z/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_y39Mfw/stacktrace.txt Please include the stack trace file in your bug report! t/04_vg_align.t ....... 1..20 not ok 1 - alignment traverses the correct path # got: '0' # expected: '4' not ok 2 - unnamed test # got: '48' # expected: 'alignment score is as expected' not ok 3 - unnamed test # got: '58' # expected: 'full length bonus works and is included by default' not ok 4 - unnamed test # got: '37' # expected: 'bonuses are included on only one end for pinned alignments' not ok 5 - unnamed test # got: '96' # expected: 'scoring parameters are respected' not ok 6 - unnamed test # got: '96' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected' not ok 7 - unnamed test # got: '70211814' # expected: 'alignment does not contain excessive soft clips under lenient scoring' not ok 8 - unnamed test # got: '70211814' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring' not ok 9 - unnamed test # got: '274' # expected: 'alignment score does not overflow at 255 when using 8x16bit vectors' not ok 10 - unnamed test # got: '274' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors' not ok 11 - unnamed test # got: '280136076' # expected: 'Ns do not cause excessive soft clipping' not ok 12 - unnamed test # got: '59867694' # expected: 'nodes are only referenced if they have mappings' not ok 13 - align can use query names and outputs GAM # got: '0' # expected: '4' not ok 14 - alignment to cyclic graphs works # got: '0' # expected: '1' not ok 15 - graphs where duplicated nodes need flipping can be used for alignment # got: '132' # expected: '0' not ok 16 - node flipping doesn't destroy the alignment # got: '132' # expected: '0' not ok 17 - alignment correctly handles an inversion # got: '132' # expected: '0' not ok 18 - the exploding graph doesn't blow up # got: '132' # expected: '0' not ok 19 - unnamed test # got: '1' # expected: 'pinning doesn't cause problems for gssw' not ok 20 - unnamed test # got: '1' # expected: 'left pinning is correctly handled' Failed 20/20 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_b5OEVn/stacktrace.txt Please include the stack trace file in your bug report! t/05_vg_find.t: line 63: 1042410 Segmentation fault (core dumped) vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam t/05_vg_find.t: line 65: 1042446 Killed vg gamsort -i x.sorted.gam.gai x.gam > x.sorted.gam error:[get_input_file] could not open file "x.sorted.gam.gai" error:[get_input_file] could not open file "x.sorted.gam.gai" WARNING:[vg] Subcommand 'combine' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/05_vg_find.t ........ 1..27 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns not ok 16 - the GAM index can return the set of alignments mapping to a node # got: '0' # expected: '6' not ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM # got: '0' # expected: '15' ok 18 - the index can be queried using GAM alignments ok 19 - find gets connected edges between queried nodes by default ok 20 - find gets nodes provided in a node file list ok 21 - extracting by path adds no extra edges ok 22 - pattern based path extraction works ok 23 - path DAG range query works ok 24 - we can extract a set of targets to separate files ok 25 - the same extraction can be made using BED input ok 26 - we see the expected number of kmers in the given targets ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 Failed 2/27 subtests t/06_vg_index.t: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8): No such file or directory WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gPVEVm/stacktrace.txt Please include the stack trace file in your bug report! t/06_vg_index.t: line 183: 1051033 Segmentation fault (core dumped) vg map -T <(vg sim -n 100 -x x.xg) -d x > x1337.gam t/06_vg_index.t: line 186: 1051071 Killed vg gamsort -i x1337.sorted.gam.gai2 x1337.gam > x1337.sorted.gam t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lqa5Rp/stacktrace.txt Please include the stack trace file in your bug report! t/06_vg_index.t ....... 1..51 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - samples can be excluded from haplotype indexing ok 19 - excluded samples were not included in the GBWT index ok 20 - GBWT from GAF same as from GAM ok 21 - building GBWT index for a regional graph ok 22 - no warnings about missing variants produced ok 23 - building an XG index of multiple graphs ok 24 - building a GCSA index of multiple graphs ok 25 - building both indexes at once ok 26 - the indexes are identical ok 27 - building a GBWT index of multiple graphs with haplotypes ok 28 - building an XG index of multiple graphs with haplotypes ok 29 - building a GCSA index of multiple graphs with haplotypes ok 30 - building XG and GCSA indexes at once ok 31 - building an XG index with alt paths ok 32 - building a GBWT index from an XG index ok 33 - the indexes are identical ok 34 - GBWT can be built for paths ok 35 - fail with nonexistent file ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used not ok 37 - vg index and vg gamsort produce identical sorted GAM indexes # got: 'c4904818dcce89724c9cef7541356be3 -' # expected: '' ok 38 - storage of multiple graphs in an index succeeds ok 39 - can index backward nodes ok 40 - can index kmers for backward nodes ok 41 - GCSA2 index works on cyclic graphs with heads and tails ok 42 - GCSA2 index works on cyclic graphs with no heads or tails ok 43 - GCSA2 index works on cyclic graphs with self loops ok 44 - GCSA2 index works on general cyclic graphs ok 45 - GCSA2 indexing of a tiny graph works ok 46 - GCSA2 indexing succeeds on a single-node graph ok 47 - GCSA2 indexing succeeds on graph with heads but no tails ok 48 - a useful error message is produced when nodes are too large not ok 49 - snarl finding with trivial snarls # got: '132' # expected: '0' ok 50 - building a distance index of a graph ok 51 - building a distance index of a graph without maximum index Failed 2/51 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0SW7ah/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_68K8N7/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KkTEJZ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pkBYXT/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_SUWFQK/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TyRRvC/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BRJytI/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_x8SS5B/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OQ2bcv/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DvMnYk/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_e8MBue/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_uI7i02/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CnsYRP/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lmhXSR/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WdwJtb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OWS6ki/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zh8lUg/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_c9D5Al/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_z7Kn39/stacktrace.txt Please include the stack trace file in your bug report! printf: usage: printf [-v var] format [arguments] ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0RA69w/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GAAQVZ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mXDHpY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6UEMT2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_AMrXmh/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zOJC5A/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GwfXID/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PnEdjC/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZKmwIX/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mhLbkv/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_wTdlZG/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Fy6eW7/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yb79q4/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_wxOGnh/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dGqn8Y/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6GMOGu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lhliOu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Wosjlt/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CO9nZP/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rkLwxY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_F9Wm8K/stacktrace.txt Please include the stack trace file in your bug report! [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_RU3pDr/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cYXhdp/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Tie4Fj/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NrmUgi/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xeJaAf/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7js1eL/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_iWUZay/stacktrace.txt Please include the stack trace file in your bug report! index file t.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6imDTw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fhTcLN/stacktrace.txt Please include the stack trace file in your bug report! t/07_vg_map.t ......... 1..54 not ok 1 - offset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 2 - xdrop alignment obtains the expected result # got: '' # expected: '3' not ok 3 - xdrop alignment obtains the expected result for the reverse complement # got: '' # expected: '5' not ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 5 - offset counts unused bases from the start of the node on the reverse strand # got: '' # expected: '5' not ok 6 - global alignment traverses the correct path # got: '0' # expected: '4' not ok 7 - alignment score is as expected # got: '' # expected: '58' not ok 8 - scoring parameters are respected # got: '' # expected: '106' not ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected # got: '' # expected: '106' not ok 10 - full length bonus always be included # got: '' # expected: '58' not ok 11 - full length bonus can be set to 0 # got: '' # expected: '96' not ok 12 - vg map takes -d as input without a variant graph # got: '132' # expected: '0' not ok 13 - vg map can align across a SNP # got: '0' # expected: '1' not ok 14 - alignment works on a small graph # got: '0' # expected: '1000' ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities not ok 17 - chunky-banded alignment works # got: '0' # expected: '1' not ok 18 - unnamed test # got: '' # expected: 'multiple alignments are returned in descending score order' not ok 19 - only a single primary alignment is returned # got: '0' # expected: '1' not ok 20 - mapping of BAM file produces expected number of alignments # got: '0' # expected: '3333' not ok 21 - mapping from a fastq produces the expected number of alignments # got: '0' # expected: '3327' ok 22 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 23 - vg connects paired-end reads in gam output not ok 24 - mapping to graphs that can't be oriented without swapping edges works correctly # got: '132' # expected: '0' not ok 25 - reads multi-map to multiple possible locations # got: '0' # expected: '1' not ok 26 - vg map works based on gcsa and xg indexes # got: '0' # expected: '1000' not ok 27 - unnamed test # got: '30' # expected: 'the mapping quality may be capped' not ok 28 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 29 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 30 - only primary alignments have mapping quality scores # got: '0' # expected: '2' not ok 31 - unpaired reads produce mapping quality scores # got: '0' # expected: '1000' ok 32 - map returns same output on xg and vg (single threaded) not ok 33 - unnamed test # got: '10' # expected: 'base quality adjusted alignment produces higher scores if mismatches have low quality' ok 34 - error on vg map -f (unpaired) ok 35 - error on vg map -f (interleaved) ok 36 - error on vg map -f (paired, LHS) ok 37 - error on vg map -f (paired, RHS) not ok 38 - mapping a read that touches unused nodes gets the base score # got: '' # expected: '36' not ok 39 - mapping a read that matches a haplotype gets a small penalty # got: '' # expected: '35' not ok 40 - mapping a read that matches a haplotype with exponent 0 gets the base score # got: '' # expected: '36' not ok 41 - mapping a read that matches no haplotypes gets a larger penalty # got: '' # expected: '21' not ok 42 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 43 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 44 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 45 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 46 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 47 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 48 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 49 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 50 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 51 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' not ok 52 - unnamed test # got: '1' # expected: 'mapper can read FASTA input' not ok 53 - unnamed test # got: '1' # expected: 'mapper can read multiline FASTA input' not ok 54 - unnamed test # got: '130' # expected: 'xdrop works on a reversed read' Failed 45/54 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2jSVh6/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_d0SWLa/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DhiRrj/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_bE2AhN/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_D5FaP5/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dLP9uG/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nX9Evi/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs not ok 4 - can sort and re-number a graph with self loops # got: '132' # expected: '0' not ok 5 - can sort and renumber a complex cyclic graph # got: '132' # expected: '0' ok 6 - sorting removes back-edges in a DAG not ok 7 - unnamed test # got: 'true' # expected: 'sorting assigns node IDs in topological order' not ok 8 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range' not ok 9 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range of vg' not ok 10 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range of hg' Failed 6/10 subtests t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes ok 2 - concat doubles the number of edges + 1 ok 3 - concat -p doubles the number of nodes on reversing graph ok 4 - concat -p doubles the number of edges + 1 on reversing graph ok t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aQ8YGR/stacktrace.txt Please include the stack trace file in your bug report! t/10_vg_stats.t: line 40: 1059609 Segmentation fault (core dumped) vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam t/10_vg_stats.t ....... 1..18 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct not ok 8 - aligned read stats are computed correctly # got: '1b5d954befa462c8f6bd2bfdc6dcbf91' # expected: 'b45c940480441a36475217a41b35e1f6' ok 9 - basic stats agree between graph formats not ok 10 - stats can be computed for GAM files without graphs # got: 'Total alignments: 0' # expected: 'Total alignments: 100' ok 11 - a path overlap description of a test graph has the expected length ok 12 - vg stats -F detects format of old protobuf graph ok 13 - vg stats -F detects format of newer protobuf graph ok 14 - vg stats -F detects format of hash graph ok 15 - vg stats -F detects format of packed graph ok 16 - vg stats -F detects format of odgi graph ok 17 - vg stats -F detects format of xg graph ok 18 - vg stats -D found correct degree distribution of tiny graph Failed 2/18 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZxEQ1v/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rk82sb/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_SlpQQJ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/11_vg_paths.t ....... 1..14 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - thread listing works from GBWT ok 4 - thread selection by name prefix works correctly ok 5 - thread selection by sample name works correctly ok 6 - no threads are reported for invalid samples ok 7 - vg paths may be used to extract threads ok 8 - vg paths may be used to extract threads as GAF ok 9 - Fasta extracted from xg is the same as the input fasta ok 10 - Fasta extracted from vg is the same as the input fasta ok 11 - Fasta extracted from threads has correct number of lines not ok 12 - a single path may be retained # got: '0' # expected: '1' ok 13 - path filtering does not modify the graph ok 14 - alt allele paths can be dropped Failed 1/14 subtests WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok index file n.fa.fai not found, generating... warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz t/13_vg_sim.t ......... 1..34 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - reads can be simulated from all paths ok 10 - simulation was successful ok 11 - reads can be simulated from GBWT samples ok 12 - simulation was successful ok 13 - pairs simulated even when fragments overlap ok 14 - sim does not emit reads with Ns ok 15 - sim can emit reads with Ns when asked to ok 16 - sim doesn't emit Ns even with pair and errors ok 17 - Sample simulation works along with --any-path ok 18 - not having any regexes skips all unvisited contigs ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig ok 22 - multiple regexes are interpreted ok 23 - regexes are interpreted as regexes ok 24 - assigning a very high ploidy by regex starves out the other paths ok 25 - Sample simulation works along with --any-path with training FASTQ ok 26 - not having any regexes skips all unvisited contigs with training FASTQ ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ ok 30 - multiple regexes are interpreted with training FASTQ ok 31 - regexes are interpreted as regexes with training FASTQ ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ ok 33 - ngs trained simulator works ok 34 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1gW8kb/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tsllSE/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WaMzyZ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fM1ty6/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PN1OVe/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fRtomv/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4KuasS/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9A1JlQ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_wLGjjf/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6gh9hz/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ngu9H3/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HDndPd/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. error[VPKG::load_one]: Correct input type not found in s.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_deUbdw/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZamIjH/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XGT4dR/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fU0E4R/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DhFKpd/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in /dev/fd/63 while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works not ok 5 - normalization produces the correct number of nodes # got: '0' # expected: '4' not ok 6 - normalization removes redundant SNP alleles # got: '0' # expected: '4' not ok 7 - normalization produces a valid graph # got: '1' # expected: '0' not ok 8 - looped normalization produces a valid graph # got: '1' # expected: '0' not ok 9 - unchop produces a valid graph # got: '1' # expected: '0' not ok 10 - unnamed test # got: '154' # expected: 'normalization removes redundant sequence in the graph' not ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '5d3999dfcafb09801e4659c1b43a8593' ok 12 - vg mod removes non-path nodes and edge ok 13 - chopping a graph works correctly with reverse mappings not ok 14 - unnamed test # got: '2f785068c91dbe84177c1fd679b6f133' # expected: 'unchop correctly handles paths' ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion not ok 18 - mod successfully unchops a difficult graph # got: '1' # expected: '0' not ok 19 - chopping self-cycling nodes retains the cycle # got: '1' # expected: '0' not ok 20 - unrolling works and produces a valid graph # got: '1' # expected: '0' not ok 21 - unfolding works and produces a valid graph # got: '1' # expected: '0' ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components not ok 25 - unfold followed by dagify produces a graph with no cycles # got: '0' # expected: '46' ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths not ok 29 - unnamed test # got: '4' # expected: 'dagify correctly calculates the minimum distance through the unrolled component' not ok 30 - unnamed test # got: '200' # expected: 'dagify produces a graph of the correct size' ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 16/32 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6TxstX/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_k5eKjO/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tABIaH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4TLMLP/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5YscW1/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pjrGau/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PiWC4f/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9ruYNx/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XDo3tD/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_n189Fu/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph Error[vg map]: Unable to open xg file "f.xg" error[VPKG::load_one]: Could not open f.xg while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nav5f5/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open f.xg while loading handlegraph::PathHandleGraph Error[vg map]: Unable to open xg file "f.xg" ERROR: Signal 4ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rEYw47/stacktrace.txt Please include the stack trace file in your bug report! occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_jotdR9/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_IZh2n8/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WCLSl9/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tfHaBa/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9ciaga/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OKXKaL/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1PbS4k/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oyOULR/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". t/15_vg_surject.t ..... 1..33 not ok 1 - reads are generated # got: '0' # expected: '100' not ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 4 - vg surject actually places reads on the correct path # got: '0' # expected: '100' not ok 5 - vg surject doesn't need to be told which path to use # got: '0' # expected: '100' not ok 6 - vg surject works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 7 - vg surject spliced algorithm works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 8 - vg surject produces valid SAM output # got: '0' # expected: '100' not ok 9 - vg map may surject reads to produce valid SAM output # got: '0' # expected: '100' not ok 10 - vg map may surject reads to produce valid BAM output # got: '0' # expected: '100' not ok 11 - vg surject retains read names # got: '0' # expected: '100' not ok 12 - vg surject can set sample and read group # got: '0' # expected: '100' not ok 13 - we respect the original mapping's softclips # got: '0' # expected: '1' ok 14 - quality strings we will use for testing are oriented correctly ok 15 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags not ok 16 - vg surject produces valid BAM output # got: '0' # expected: '100' ok 17 - mapping quality is preserved through surjection ok 18 - read pairing is preserved through GAM->GAM surjection ok 19 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 25 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 26 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' not ok 27 - surjection works for a longer (151bp) read # got: '0' # expected: '1' not ok 28 - surjection works for another difficult read # got: '0' # expected: '1' not ok 29 - mapping reproduces qualities from BAM input # got: '0' # expected: '1' not ok 30 - mapping reproduces qualities from fastq input # got: '0' # expected: '1' not ok 31 - mapping reproduces qualities from GAF input # got: '0' # expected: '1' not ok 32 - surject works on GAMP input # got: '0' # expected: '1000' not ok 33 - surject works on paired GAMP input # got: '0' # expected: '1000' Failed 28/33 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DdRw7F/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Ndi1ko/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_AdE683/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xMIxHw/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Xmz6lS/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cF5OYD/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. error[VPKG::load_one]: Correct input type not found in s.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4cE2bw/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nFSLaV/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5He124/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9Wq3Td/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/inv.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Qrpwgt/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YhjayP/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JW33y0/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_C72Ib8/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/16_vg_msga.t ........ 1..14 not ok 1 - MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '16e56f0090b310d2b1479d49cf790324' not ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '2ab075dd73c31ea9939726d72c12655f' not ok 3 - soft clips at node boundaries (start) are included correctly # got: '0' # expected: '1' not ok 4 - soft clips at node boundaries (end) are included correctly # got: '0' # expected: '1' ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph not ok 7 - the paths of the graph encode the original sequences used to build it # got: '0' # expected: '2' not ok 8 - even when banding the paths of the graph encode the original sequences used to build it # got: '1' # expected: '0' not ok 9 - HLA K-3138 correctly includes all input paths # got: '1' # expected: '0' not ok 10 - a difficult cyclic path can be included to produce a valid graph # got: '1' # expected: '0' not ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected # got: '0' # expected: '1' not ok 12 - edges in cycles with two nodes are correctly included # got: '1' # expected: '0' not ok 13 - HLA B-3106 is assembled into a valid graph # got: '1' # expected: '0' not ok 14 - odd-sized overlaps may be used for chunked alignment # got: '1' # expected: '0' Failed 12/14 subtests [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yLXskD/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xeK1gz/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_iN1F3v/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PPFw1W/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KtM8kU/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZJLumW/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fTSIl5/stacktrace.txt Please include the stack trace file in your bug report! Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hQgRnj/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7tLHrP/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1EiGv8/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_bLEX56/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_F2CZth/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hEXFUR/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rTtuVm/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Z8ZKvy/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ZhUEH1/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_U7OcsE/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HsWKSN/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1XfXSj/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9zmhER/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9ogpj7/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2PWKXG/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DuqMam/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Quf4vC/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DWeuob/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lic9YS/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kzGNJt/stacktrace.txt Please include the stack trace file in your bug report! t/17_vg_augment.t ..... 1..39 ok 1 - direct augmentation embeds reads fully for well-supported SNPs ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes ok 6 - direct augmentation embeds reads fully for probable errors ok 7 - adding a probable error by direct augmentation adds 3 more nodes ok 8 - path inclusion does not modify the graph when alignment is a perfect match ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold not ok 11 - output GAM has single edit when SNP was filtered out due to coverage # got: '0' # expected: '1' not ok 12 - path inclusion with a complex variant introduces the right number of nodes # got: '1' # expected: '5' not ok 13 - path inclusion works for deletions # got: '0' # expected: '1' not ok 14 - SNPs can be included in the graph # got: '1' # expected: '4' not ok 15 - unnamed test # got: 'GGGGG' # expected: 'a soft clip at read start becomes a new head of the graph' not ok 16 - unnamed test # got: 'AAAAAAAA' # expected: 'a soft clip at read end becomes a new tail of the graph' not ok 17 - augment -s works as desired # got: '0' # expected: '1' not ok 18 - the expected graph translation is exported when the graph is edited # got: '420' # expected: '1290' not ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes # got: '0' # expected: '7' ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps not ok 22 - augmenting with 2snps makes correct number of nodes # got: '1' # expected: '7' not ok 23 - low-quality snp is filtered # got: '1' # expected: '4' ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph 2a3 > GGNGG not ok 26 - augmenting between nodes without filters works as expected # got: '1' # expected: '0' 2a3 > GGNGG not ok 27 - augmenting between nodes with inactive filters works as expected # got: '1' # expected: '0' ok 28 - augmenting between nodes N filter works as expected 2a3 > GGNGG not ok 29 - augmenting between nodes without filters works as expected on reverse strand # got: '1' # expected: '0' 2a3 > GGNGG not ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand # got: '1' # expected: '0' ok 31 - augmenting between nodes N filter works as expected on reverse strand not ok 32 - augmenting within node without filters works as expected # got: '0' # expected: '1' not ok 33 - augmenting within node with inactive filters works as expected # got: '0' # expected: '1' ok 34 - augmenting within node with N filter works as expected not ok 35 - augmenting within node without filters works as expected on reverse strand # got: '0' # expected: '1' not ok 36 - augmenting within node with inactive filters works as expected on reverse strand # got: '0' # expected: '1' ok 37 - augmenting within node with N filter works as expected on reverse strand not ok 38 - unnamed test # got: 'CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG' # expected: 'sequence in filtered alignment has removed insertion' not ok 39 - unnamed test # got: 'CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG' # expected: 'sequence in filtered alignment has removed insertion on reverse strand' Failed 21/39 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aRRZBL/stacktrace.txt Please include the stack trace file in your bug report! index file inverting/miniFasta.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8jhsr7/stacktrace.txt Please include the stack trace file in your bug report! t/18_vg_call.t: line 29: 1115580 Segmentation fault (core dumped) vg map -G miniFasta.gam -g miniFastaGraph.gcsa -x miniFastaGraph.xg > miniFastaGraph.gam ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Be6Tok/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_D6Meny/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2WFo7J/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Q0est2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_T8zlNy/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YQ3pic/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_08wRFb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_69qP5V/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_V65lcs/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YEHXfk/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Nz8gMV/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph index file m.fa.fai not found, generating... Error[vg map]: Unable to open xg file "c.xg" error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open c.aug.xg while loading handlegraph::HandleGraph error:[get_input_file] could not open file "c.aug.xg" ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_k7WECi/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ryBlN9/stacktrace.txt Please include the stack trace file in your bug report! t/18_vg_call.t ........ 1..12 ok 1 - calling empty gam gives empty VCF not ok 2 - Called microinversion # got: '0' # expected: '1' ok 3 - Called no microinversion with haploid setting not ok 4 - Fewer than 8 differences between called and true SV genotypes # got: '0' # expected: '1' not ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes # got: '0' # expected: '1' ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg not ok 11 - vg call finds true homozygous variants in a cyclic graph # got: '0' # expected: '3' ok 12 - vg call finds same variants when using gbwt to enumerate traversals Failed 4/12 subtests t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok t/21_vg_filter.t ...... 1..10 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - read pairs can be tropped by feature ok 10 - read pairs can be kept if only one read fails ok t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aUo8u2/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oXshHR/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "hla.xg" error:[get_input_file] could not open file "hla.xg" error:[get_input_file] could not open file "hla.xg" ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BwDX2q/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_40NO5e/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3uNyLO/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_K4JeCB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_SSFcGM/stacktrace.txt Please include the stack trace file in your bug report! graph path 'alt2.3' invalid: edge from 15 end to 1 start does not exist [vg view] warning: graph is invalid! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LfTrex/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Un6W84/stacktrace.txt Please include the stack trace file in your bug report! t/26_deconstruct.t .... 1..19 1,3d0 < x 14 G A < x 34 T A < x 39 T A not ok 1 - deconstruct retrieved original VCF (modulo adjacent snp allele) # got: '1' # expected: '0' not ok 2 - deconstructed hla vcf has correct number of sites # got: '0' # expected: '17' not ok 3 - unnamed test # got: 'C-CGCGGGCGCCGTGGATGGAGCA' # expected: 'deconstructed hla vcf has correct insertion' not ok 4 - deconstructed hla vcf with other path has correct number of sites # got: '0' # expected: '17' not ok 5 - unnamed test # got: 'CGCGGGCGCCGTGGATGGAGCA-C' # expected: 'deconstructed hla vcf has correct deletion' ok 6 - path-based and exhaustive decontruction give equivalent sites when expected not ok 7 - unnamed test # got: '1' # expected: 'path that differs from reference in every alt has correct genotype' not ok 8 - unnamed test # got: '0' # expected: 'path that is same as reference in every alt has correct genotype' not ok 9 - unnamed test # got: '##contig=' # expected: 'reference contig correctly written' 0a1 > x 10 CTTGGAAATTTTCTGGAGTT AACTCCAGAAAATTTCCAAG 1 not ok 10 - deconstruct correctly handles a simple inversion # got: '1' # expected: '0' 0a1 > y 10 AACTCCAGAAAATTTCCAAG CTTGGAAATTTTCTGGAGTT 1 not ok 11 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge # got: '1' # expected: '0' 0a1 > y 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA 1 not ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl # got: '1' # expected: '0' 0a1 > x 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA 1 not ok 13 - deconstruct correctly handles a cycle in the alt path # got: '1' # expected: '0' not ok 14 - cyclic reference deconstruction has correct number of variants # got: '0' # expected: '2' 0a1,2 > y 20 T A 0 > y 44 A T 1 not ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl # got: '1' # expected: '0' not ok 16 - -P -A options return correct number of variants # got: '0' # expected: '2' not ok 17 - -P -A options use correct reference name # got: '0' # expected: '2' not ok 18 - -P -A identifies conflict in alt1 in second variant # got: '0' # expected: '1' ok 19 - deconstructing vg graph gives same output as xg graph Failed 17/19 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_SMlcaD/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t: line 14: 1132276 Segmentation fault (core dumped) vg map -T reads.txt -g tiny.vg.gcsa -x tiny.vg.xg > tiny.gam ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pHd6Ql/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YLfyWq/stacktrace.txt Please include the stack trace file in your bug report! index file flat1.fa.fai not found, generating... index file flat2.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LnG8iA/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TZ3Fcm/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file flats.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_W5efov/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tdRtyY/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5hhQwn/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t: line 54: 1134230 Segmentation fault (core dumped) vg map -T reads.txt -g bigins.vg.gcsa -x bigins.vg.xg > bigins.gam ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JArtO8/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t .... 1..5 not ok 1 - vg genotype runs successfully # got: '132' # expected: '0' not ok 2 - vg genotype runs successfully when emitting vcf # got: '132' # expected: '0' ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON not ok 5 - genotype finds big insert # got: '0' # expected: '1' Failed 3/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2sV5xi/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nSmneN/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gqAfys/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JzItJu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vRlSmq/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end t/30_vg_chunk.t ....... 1..24 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk has path going through node 9 ok 5 - -s produces correct number of chunks ok 6 - gam chunker produces correct number of graphs ok 7 - gam chunker produces correct number of gams ok 8 - gam chunker produces bed with correct number of chunks ok 9 - gam chunker emits each matching read at most once ok 10 - chunk contains the expected number of alignments ok 11 - id chunker produces correct chunk size ok 12 - id chunker produces correct single chunk ok 13 - id chunker traces correct chunk size ok 14 - chunker extracts no threads from an empty gPBWT ok 15 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 16 - chunker can extract a partial haplotype from a GBWT ok 17 - n-chunking works and chunks over the full graph ok 18 - path-based components finds subgraphs ok 19 - x gam chunk has correct number of reads ok 20 - y gam chunk has correct number of reads ok 21 - x gam chunk has correct number of reads with -p path ok 22 - y gam chunk has correct number of reads with -p path ok 23 - path-based component contains correct path length ok 24 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_60Q8RH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_FrkZX5/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sz9ABI/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mJIsKc/stacktrace.txt Please include the stack trace file in your bug report! index file add/refN.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_20EQ2H/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph index file add/ngap.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_A3fYmM/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in ngap-add.vg while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CldHhb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BWdlx4/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OawYrK/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TxwiKt/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..12 not ok 1 - vg add can create a graph # got: '132' # expected: '0' not ok 2 - vg add can create a graph with contig renames # got: '132' # expected: '0' ok 3 - vg add produces the same graph from VCFs with different contig names not ok 4 - vg add can create a graph from a PackedGraph # got: '132' # expected: '0' ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology not ok 7 - adding variants adds only the alt bases near large N gaps # got: '' # expected: '73315' not ok 8 - vg add can create a slightly larger graph # got: '132' # expected: '0' ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 8/12 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8YtRTm/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zqBh9y/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_RklGSE/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_jQGzVN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GfwPuw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_05hsUI/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_m6NJxu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zNuOoF/stacktrace.txt Please include the stack trace file in your bug report! Restricting to x from 1 to end Restricting to y from 1 to end ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XQ5GKw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_jACOwN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_F8A1z2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_94jFae/stacktrace.txt Please include the stack trace file in your bug report! t/32_vg_snarls.t ...... 1..9 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 4 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 5 - vcf traversals are the same as exhaustive traversals for tiny graph ok 6 - vcf traversals are the same as exhaustive traversals for inversion ok 7 - vcf traversals are the same as exhaustive traversals for ins_and_del graph not ok 8 - correct number of snarls when parallelizing on compoents # got: '0' # expected: '35' ok 9 - same number of snarls when parallelizing on components Failed 5/9 subtests [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.match.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_50b6ka/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.match.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Sm1V99/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.matchpaired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TLoGzi/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.matchpaired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VS8WIj/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cxTrtP/stacktrace.txt Please include the stack trace file in your bug report! warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hjv5dU/stacktrace.txt Please include the stack trace file in your bug report! warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oexM0T/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 1 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_qdeBcX/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gcV50I/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 10 -D 50 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_eG7jZ3/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 100000 -D 5 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_MTQpsV/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4cBX6L/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from input.gam using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sRFDU8/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0.0 s: Loading graph from t.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from t.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XPk6FL/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oT5FjT/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_x2PyEX/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cNqj0a/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tBPDHm/stacktrace.txt Please include the stack trace file in your bug report! t/33_vg_mpmap.t ....... 1..17 not ok 1 - MAPQ is 50% without haplotype info # got: '' # expected: '3' not ok 2 - haplotype match can disambiguate # got: '' # expected: '4' not ok 3 - MAPQ is 50% when paired without haplotype info # got: '' # expected: '3' not ok 4 - haplotype match can disambiguate paired # got: '' # expected: '4' not ok 5 - use of haplotype-aware mapping is recorded # got: '' # expected: 'true' not ok 6 - Haplotype-oblivious mapping places read on the wrong contig # got: '' # expected: '50' not ok 7 - Haplotype-oblivious mapping places read with MAPQ of 50% # got: '' # expected: '3' not ok 8 - Haplotype-aware mapping places read on the right contig # got: '' # expected: '1' not ok 9 - Haplotype-aware mapping places read with MAPQ > 50% # got: '' # expected: '6' not ok 10 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 11 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 12 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart # got: '0' # expected: '1' ok 13 - small batches are still all paired in the output not ok 14 - multipath mapping works in scenarios that trigger branch point trimming # got: '0' # expected: '3' not ok 15 - spliced alignments can be found when aligning RNA # got: '' # expected: '108' not ok 16 - paired mapping can identify a splice junction on read 1 # got: '0' # expected: '1' not ok 17 - paired mapping can identify a splice junction on read 2 # got: '0' # expected: '1' Failed 16/17 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_EChxLQ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sRKjEm/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KxBtPP/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9ahX4a/stacktrace.txt Please include the stack trace file in your bug report! t/34_vg_pack.t ........ 1..18 not ok 1 - allele observation packing detects 2 SNPs # got: '0' # expected: '2' ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - average node qualities are correct # got: '0-0-0-0-0-0-0-0-0-0-' # expected: '20-15-10-10-0-0-0-0-60-60-' Failed 2/18 subtests t/36_vg_annotate.t .... 1..9 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature ok 7 - annotating with earliest path position produces one position ok 8 - annotating with multiple path positions produces multiple positions ok 9 - annotations derived from BED can span the end/start joins of circular paths ok t/37_vg_gbwt.t ........ 1..91 ok 1 - chromosome X GBWT with vg gbwt ok 2 - chromosome X GBWT with vg index ok 3 - identical construction results with vg gbwt and vg index ok 4 - chromosome X VCF parse ok 5 - chromosome X GBWT from VCF parse ok 6 - identical construction results with vg gbwt and from VCF parse ok 7 - chromosome X: 2 threads ok 8 - chromosome X: 1 contig ok 9 - chromosome X: 2 haplotypes ok 10 - chromosome X: 1 sample ok 11 - chromosome X: 2 thread names ok 12 - chromosome X: 1 contig name ok 13 - chromosome X: 1 sample name ok 14 - chromosome X reference GBWT with vg gbwt ok 15 - chromosome X reference GBWT with vg index ok 16 - identical construction results with vg gbwt and vg index ok 17 - chromosome X reference: 1 thread ok 18 - chromosome X GAF with vg gbwt ok 19 - chromosome X GAF with vg index ok 20 - identical construction results with vg gbwt and vg index ok 21 - chromosome X GAM with vg gbwt ok 22 - identical construction results from GAF and GAM ok 23 - chromosome X subgraph GBWT with vg gbwt ok 24 - no warnings about missing variants ok 25 - chromosome X subgraph GBWT with vg index ok 26 - identical construction results with vg gbwt and vg index ok 27 - insertion merging with multiple chromosomes ok 28 - fast merging with multiple chromosomes ok 29 - identical merging results with the insertion and fast algorithms ok 30 - parallel merging with multiple chromosomes ok 31 - identical merging results with the insertion and parallel algorithms ok 32 - direct construction with multiple chromosomes and a single VCF ok 33 - identical results with direct construction and merging ok 34 - direct construction with multiple chromosomes and multiple VCFs ok 35 - identical construction results with a single VCF and multiple VCFs ok 36 - construction preset: 1000gp ok 37 - multiple chromosomes: 4 threads ok 38 - multiple chromosomes: 2 contigs ok 39 - multiple chromosomes: 2 haplotypes ok 40 - multiple chromosomes: 1 sample ok 41 - paths as contigs with vg gbwt ok 42 - paths as contigs with vg index ok 43 - identical construction results with vg gbwt and vg index ok 44 - paths as contigs: 2 threads ok 45 - paths as contigs: 2 contigs ok 46 - paths as contigs: 1 haplotype ok 47 - paths as contigs: 1 sample ok 48 - paths as samples with vg gbwt ok 49 - paths as samples with vg index ok 50 - paths as samples: 2 threads ok 51 - paths as samples: 1 contig ok 52 - paths as samples: 2 haplotypes ok 53 - paths as samples: 2 samples ok 54 - r-index construction ok 55 - normal merging: non-empty + empty ok 56 - the index remains unchanged ok 57 - normal merging: empty + non-empty ok 58 - the index remains unchanged ok 59 - fast merging: non-empty + empty ok 60 - the index remains unchanged ok 61 - fast merging: empty + non-empty ok 62 - the index remains unchanged ok 63 - parallel merging: non-empty + empty ok 64 - the index remains unchanged ok 65 - parallel merging: empty + non-empty ok 66 - the index remains unchanged ok 67 - haplotypes and paths: 6 threads ok 68 - samples can be removed from a GBWT index ok 69 - haplotypes only: 4 threads ok 70 - threads can be extracted from GBWT ok 71 - correct size for the thread file ok 72 - GBWTGraph construction was successful ok 73 - GBWTGraph was correctly serialized ok 74 - Path cover GBWTGraph construction was successful ok 75 - GBWTGraph was correctly serialized ok 76 - path cover: 32 threads ok 77 - path cover: 2 contigs ok 78 - path cover: 16 haplotypes ok 79 - path cover: 16 samples ok 80 - Local haplotypes GBWTGraph construction was successful ok 81 - GBWTGraph was correctly serialized ok 82 - local haplotypes: 32 threads ok 83 - local haplotypes: 2 contigs ok 84 - local haplotypes: 16 haplotypes ok 85 - local haplotypes: 16 samples ok 86 - Augmented GBWTGraph construction was successful ok 87 - GBWTGraph was correctly serialized ok 88 - augmented: 18 threads ok 89 - augmented: 2 contigs ok 90 - augmented: 2 haplotypes ok 91 - augmented: 17 samples ok t/38_vg_prune.t ....... 1..18 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - empty mapping starts from the right node id ok 17 - the first unfolded graph adds the correct number of nodes to the mapping ok 18 - the second unfolded graph adds the correct number of nodes to the mapping ok t/39_vg_inject.t ...... 1..10 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9BznJz/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0uOQWG/stacktrace.txt Please include the stack trace file in your bug report! 1000 reads correct ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XyOwqK/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lFD0Ms/stacktrace.txt Please include the stack trace file in your bug report! 0 reads correct 0 reads correct 0 reads correct t/40_vg_gamcompare.t .. 1..5 not ok 1 - gamcompare completes # got: '0' # expected: '1000' ok 2 - gamcompare says the truth is correctly mapped not ok 3 - Reads annotated with leftmost position only are close enough at a long distance # got: '0' # expected: '1' ok 4 - Reads annotated with leftmost position only are too far apart at a short distance not ok 5 - Reads annotated with multiple positions only are close enough at a short distance # got: '0' # expected: '1' Failed 3/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_E5bRFW/stacktrace.txt Please include the stack trace file in your bug report! t/41_vg_viz.t ......... 1..1 ok 1 - vg viz runs ok t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_qO0iI4/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/43_vg_simplify.t .... 1..5 not ok 1 - vg simplify runs through when popping small bubbles # got: '132' # expected: '0' not ok 2 - simplification pops all the bubbles in a simple graph # got: '' # expected: '1' ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants not ok 5 - simplification keeps only some variants # got: '' # expected: '118' Failed 3/5 subtests t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kIIVx2/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/45_vg_sort.t ........ 1..5 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing not ok 3 - a vg graph can be sorted topologically # got: '132' # expected: '0' ok 4 - a vg graph can be sorted with Eades algorithm without crashing ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing Failed 1/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VLPvXb/stacktrace.txt Please include the stack trace file in your bug report! warning: [vg index] providing input XG with option -x is deprecated t/46_vg_minimizer.t ... 1..14 ok 1 - default parameters ok 2 - single-threaded construction ok 3 - construction is deterministic ok 4 - syncmer index ok 5 - construction is deterministic ok 6 - minimizer parameters ok 7 - setting -k -w works correctly ok 8 - construction from GBWTGraph ok 9 - construction is deterministic ok 10 - construction with payload not ok 11 - construction is deterministic # got: '58b2bd98902df9acbe416bcfde649571' # expected: '58a6780c18921e4f6701b57fdb9c2e44' ok 12 - multiple graphs: first ok 13 - multiple graphs: second ok 14 - construction is deterministic Failed 1/14 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3gilnI/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open hla.xg while loading handlegraph::PathHandleGraph t/47_vg_dotplot.t ..... 1..1 not ok 1 - vg dotplot runs successfully # got: '1' # expected: '0' Failed 1/1 subtests warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7OKopb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8vESKg/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_SAQLCl/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4nhuoi/stacktrace.txt Please include the stack trace file in your bug report! warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. t/48_vg_convert.t ..... 1..26 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout ODGI conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - odgi conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 14 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 15 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 17 - vg convert gam -> gaf -> gam preserves sequence ok 18 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 19 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 20 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads ok 21 - split alignment converted using deletions to represent internal offsets ok 22 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 23 - convert gam->gaf->gam on softclipped read preserves sequence ok 24 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 25 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_j3ZtfG/stacktrace.txt Please include the stack trace file in your bug report! t/49_vg_depth.t ....... 1..4 not ok 1 - vg depth gets correct depth from gam # got: 'nan' # expected: '18' not ok 2 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from pack' not ok 3 - vg depth gets correct number of bins # got: '0' # expected: '5' not ok 4 - vg depth gets correct depth from gaf # got: 'nan' # expected: '18' Failed 4/4 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VlIZOO/stacktrace.txt Please include the stack trace file in your bug report! index file x.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sEkaph/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gKJL8E/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_68P7Qz/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Fp5mWu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7Gb7Rb/stacktrace.txt Please include the stack trace file in your bug report! index file xy.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0kbD79/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HylvBr/stacktrace.txt Please include the stack trace file in your bug report! t/50_vg_giraffe.t ..... 1..20 ok 1 - a read can be mapped with all indexes specified without crashing ok 2 - a read can be mapped with syncmer indexes without crashing not ok 3 - a read can be mapped with just FASTA and VCF without crashing # got: '132' # expected: '0' not ok 4 - mapping with just a FASTA and a VCF produced JSON-able alignments # got: '1' # expected: '0' 1d0 < {"annotation": {"mapq_explored_cap": 57.653475280336039, "mapq_uncapped": 3, "secondary_scores": [63, 63]}, "identity": 0.96825396825396826, "mapping_quality": 3, "name": "read", "path": {"mapping": [{"edit": [{"from_length": 1, "sequence": "T", "to_length": 1}], "position": {"node_id": "96"}, "rank": "1"}, {"edit": [{"from_length": 2, "to_length": 2}], "position": {"node_id": "98"}, "rank": "2"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "100"}, "rank": "3"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"node_id": "101"}, "rank": "4"}, {"edit": [{"from_length": 26, "to_length": 26}], "position": {"node_id": "102"}, "rank": "5"}, {"edit": [{"from_length": 1, "sequence": "C", "to_length": 1}], "position": {"node_id": "104"}, "rank": "6"}]}, "quality": "QkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJC", "score": 63, "sequence": "TTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCC"} not ok 5 - mapping to manually-generated indexes and automatically-generated indexes is the same # got: '1' # expected: '0' ok 6 - mapping with syncmers produces the same alignment as mapping with minimizers not ok 7 - unpaired reads lack cross-references # got: '0' # expected: '1000' ok 8 - paired reads have cross-references not ok 9 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 10 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 11 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 12 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 13 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 14 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 15 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 16 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 17 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 18 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:y LN:1001 > @SQ SN:x LN:1001 not ok 19 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order # got: '1' # expected: '0' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:x LN:1001 > @SQ SN:y LN:1001 not ok 20 - surjecting with a sequence dictionary in sorted order produces headers in sorted order # got: '1' # expected: '0' Failed 16/20 subtests Test Summary Report ------------------- t/00_unittest.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/02_vg_construct.t (Wstat: 0 Tests: 28 Failed: 1) Failed test: 25 t/04_vg_align.t (Wstat: 0 Tests: 20 Failed: 20) Failed tests: 1-20 t/05_vg_find.t (Wstat: 0 Tests: 27 Failed: 2) Failed tests: 16-17 t/06_vg_index.t (Wstat: 0 Tests: 51 Failed: 2) Failed tests: 37, 49 t/07_vg_map.t (Wstat: 0 Tests: 54 Failed: 45) Failed tests: 1-14, 17-21, 24-31, 33, 38-54 t/08_vg_ids.t (Wstat: 0 Tests: 10 Failed: 6) Failed tests: 4-5, 7-10 t/10_vg_stats.t (Wstat: 0 Tests: 18 Failed: 2) Failed tests: 8, 10 t/11_vg_paths.t (Wstat: 0 Tests: 14 Failed: 1) Failed test: 12 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 16) Failed tests: 5-11, 14, 16, 18-21, 25, 29-30 t/15_vg_surject.t (Wstat: 0 Tests: 33 Failed: 28) Failed tests: 1-13, 16, 20-33 t/16_vg_msga.t (Wstat: 0 Tests: 14 Failed: 12) Failed tests: 1-4, 7-14 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 21) Failed tests: 11-19, 22-23, 26-27, 29-30, 32-33, 35-36 38-39 t/18_vg_call.t (Wstat: 0 Tests: 12 Failed: 4) Failed tests: 2, 4-5, 11 t/26_deconstruct.t (Wstat: 0 Tests: 19 Failed: 17) Failed tests: 1-5, 7-18 t/27_vg_genotype.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1-2, 5 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 8) Failed tests: 1-2, 4, 7-8, 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 9 Failed: 5) Failed tests: 1-4, 8 t/33_vg_mpmap.t (Wstat: 0 Tests: 17 Failed: 16) Failed tests: 1-12, 14-17 t/34_vg_pack.t (Wstat: 0 Tests: 18 Failed: 2) Failed tests: 1, 18 t/40_vg_gamcompare.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1, 3, 5 t/43_vg_simplify.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1-2, 5 t/45_vg_sort.t (Wstat: 0 Tests: 5 Failed: 1) Failed test: 3 t/46_vg_minimizer.t (Wstat: 0 Tests: 14 Failed: 1) Failed test: 11 t/47_vg_dotplot.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/49_vg_depth.t (Wstat: 0 Tests: 4 Failed: 4) Failed tests: 1-4 t/50_vg_giraffe.t (Wstat: 0 Tests: 20 Failed: 16) Failed tests: 3-5, 7, 9-20 Files=49, Tests=758, 15377 wallclock secs ( 0.71 usr 0.14 sys + 10991.02 cusr 987.94 csys = 11979.81 CPU) Result: FAIL Testing /build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx2 '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-avx2' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg' t/00_unittest.t: line 12: 1192900 Illegal instruction (core dumped) vg test t/00_unittest.t ....... 1..1 not ok 1 - vg unit tests complete successfully # got: '132' # expected: '0' Failed 1/1 subtests t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok t/02_vg_construct.t: line 18: 1192921 Illegal instruction (core dumped) vg construct -m 1000 -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg t/02_vg_construct.t: line 31: 1192936 Illegal instruction (core dumped) vg construct -m 1000 -r complex/c.fa -v complex/c.vcf.gz > c.vg t/02_vg_construct.t: line 47: 1192954 Illegal instruction (core dumped) vg construct -r order/n.fa -v order/z.vcf.gz -R n:47-73 > /dev/null t/02_vg_construct.t: line 70: 1194573 Illegal instruction (core dumped) vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz -R z:10-20 > /dev/null t/02_vg_construct.t: line 97: 1194914 Illegal instruction (core dumped) vg construct -r small/x.fa > /dev/null t/02_vg_construct.t: line 109: 1194943 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.v4.3.vcf.gz > x.vg t/02_vg_construct.t: line 113: 1194945 Illegal instruction (core dumped) vg construct -r tiny/ambiguous.fa > tiny.vg t/02_vg_construct.t ... 1..28 not ok 1 - unnamed test # got: '210' # expected: 'construction produces the right number of nodes' not ok 2 - unnamed test # got: '291' # expected: 'construction produces the right number of edges' not ok 3 - unnamed test # got: '2' # expected: 'construction obeys rename and region options' not ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds # got: '132' # expected: '0' not ok 5 - unnamed test # got: '84559' # expected: 'the 1mb graph has the expected number of nodes' not ok 6 - unnamed test # got: '115375' # expected: 'the 1mb graph has the expected number of edges' ok 7 - node size is manageable by default not ok 8 - construction of a very complex region succeeds # got: '132' # expected: '0' not ok 9 - unnamed test # got: '71' # expected: 'the complex graph has the expected number of nodes' not ok 10 - unnamed test # got: '116' # expected: 'the complex graph has the expected number of edges' ok 11 - the ordering of variants at the same position has no effect on the resulting graph not ok 12 - construction does not fail when the first position in the VCF is repeated and has an indel # got: '132' # expected: '0' ok 13 - the size of the regions used in construction has no effect on the graph ok 14 - the number of threads used in construction has no effect on the graph ok 15 - the number of threads and regions used in construction has no effect on the graph not ok 16 - construction of a graph with two head nodes succeeds # got: '132' # expected: '0' not ok 17 - unnamed test # got: '1074' # expected: 'the graph contains all the sequence in the reference and VCF' not ok 18 - varying the max node size does not affect graph length # got: '0' # expected: '1' not ok 19 - unnamed test # got: '12' # expected: 'nodes are correctly capped in size' not ok 20 - unnamed test # got: '241' # expected: '-R --region flag is respected' not ok 21 - vg construct does not require a vcf # got: '132' # expected: '0' ok 22 - vg construct respects node size limit not ok 23 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) # got: '0' # expected: '1' not ok 24 - vg constructs the correct graph for inversions # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'be12a6d186b521aee08d3eda102490ca' not ok 25 - vg construct skips variants with . ALTs # got: '' # expected: '1' not ok 26 - VCF with * alleles is rejected # got: '132' # expected: '1' not ok 27 - Reference with ambiguity codes has them coerced to Ns # got: '132' # expected: '0' not ok 28 - Expected number of Ns are created # got: '0' # expected: '10' Failed 22/28 subtests t/03_vg_view.t: line 21: 1194993 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz 1194994 (core dumped) | vg view -Vg - 1194995 Illegal instruction | vg view -Fv - > x.vg t/03_vg_view.t: line 45: 1195032 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz 1195033 (core dumped) | vg view -v - > x.vg t/03_vg_view.t: line 52: 1195043 Illegal instruction (core dumped) vg view -Fv overlaps/two_snvs_assembly1.gfa > /dev/null 2> errors.txt t/03_vg_view.t: line 56: 1195047 Illegal instruction (core dumped) vg view -Fv overlaps/incorrect_overlap.gfa > /dev/null 2> errors.txt t/03_vg_view.t ........ 1..19 not ok 1 - view produces the expected number of lines of dot output # got: '0' # expected: '505' not ok 2 - view produces the expected number of lines of GFA output # got: '0' # expected: '503' not ok 3 - view converts back and forth between GFA and vg format # got: '0' # expected: '10' not ok 4 - view can convert BAM to GAM # got: '0' # expected: '3333' ok 5 - view can round-trip JSON and GAM ok 6 - view can reconstruct a VG graph from JSON ok 7 - view can pass through VG when loading as vg::VG ok 8 - view can pass through semantically identical VG normally ok 9 - view parses sample names not ok 10 - view can handle fastq input # got: '0' # expected: '2000' not ok 11 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' not ok 12 - view outputs properly oriented GFA # got: '0' # expected: '1' not ok 13 - view produces the expected number of lines of dot output from a cyclic graph # got: '0' # expected: '23' not ok 14 - streaming JSON output produces the expected number of chunks # got: '0' # expected: '4' ok 15 - duplicate warnings can be suppressed when loading as vg::VG not ok 16 - gfa graphs with overlaps are rejected # got: '132' # expected: '1' not ok 17 - GFA import produces a concise error message when overlaps are present # got: '0' # expected: '2' not ok 18 - GFA import rejects a GFA file with an overlap that goes beyond its sequences # got: '132' # expected: '1' not ok 19 - GFA import produces a concise error message in that case # got: '0' # expected: '2' Failed 13/19 subtests t/04_vg_align.t: line 10: 1195053 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/04_vg_align.t: line 38: 1195099 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa > t.vg t/04_vg_align.t: line 40: 1195100 Illegal instruction (core dumped) vg align -s $seq t.vg 1195101 (core dumped) | vg augment t.vg - -i -S > t2.vg t/04_vg_align.t: line 47: 1195117 Illegal instruction (core dumped) vg align -s ACGT -j cyclic/reverse_self.vg > /dev/null t/04_vg_align.t: line 50: 1195118 Illegal instruction (core dumped) vg align -s AGTCCTTGAAAGAGGGCAAAATAAACTGTTAGTAGAGCCAGGTCTGAAAACAACACTTTCTTGC inverting/m.vg > /dev/null t/04_vg_align.t: line 53: 1195119 Illegal instruction (core dumped) vg align -s ATTTTTAACTCCATGTTTGAGAAACATTTAATAATGTAATGTGTTTGTGGCACAGCAGGAGTAC graphs/difficult-inv.vg > /dev/null t/04_vg_align.t: line 56: 1195120 Illegal instruction (core dumped) vg align -s AAACATACATTTTC graphs/exploding.vg > /dev/null t/04_vg_align.t ....... 1..20 not ok 1 - alignment traverses the correct path # got: '0' # expected: '4' not ok 2 - unnamed test # got: '48' # expected: 'alignment score is as expected' not ok 3 - unnamed test # got: '58' # expected: 'full length bonus works and is included by default' not ok 4 - unnamed test # got: '37' # expected: 'bonuses are included on only one end for pinned alignments' not ok 5 - unnamed test # got: '96' # expected: 'scoring parameters are respected' not ok 6 - unnamed test # got: '96' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected' not ok 7 - unnamed test # got: '70211814' # expected: 'alignment does not contain excessive soft clips under lenient scoring' not ok 8 - unnamed test # got: '70211814' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring' not ok 9 - unnamed test # got: '274' # expected: 'alignment score does not overflow at 255 when using 8x16bit vectors' not ok 10 - unnamed test # got: '274' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors' not ok 11 - unnamed test # got: '280136076' # expected: 'Ns do not cause excessive soft clipping' not ok 12 - unnamed test # got: '59867694' # expected: 'nodes are only referenced if they have mappings' not ok 13 - align can use query names and outputs GAM # got: '0' # expected: '4' not ok 14 - alignment to cyclic graphs works # got: '0' # expected: '1' not ok 15 - graphs where duplicated nodes need flipping can be used for alignment # got: '132' # expected: '0' not ok 16 - node flipping doesn't destroy the alignment # got: '132' # expected: '0' not ok 17 - alignment correctly handles an inversion # got: '132' # expected: '0' not ok 18 - the exploding graph doesn't blow up # got: '132' # expected: '0' not ok 19 - unnamed test # got: '1' # expected: 'pinning doesn't cause problems for gssw' not ok 20 - unnamed test # got: '1' # expected: 'left pinning is correctly handled' Failed 20/20 subtests t/05_vg_find.t: line 10: 1195128 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/05_vg_find.t: line 13: 1195129 Illegal instruction (core dumped) vg index -x x.xg x.vg 2> /dev/null t/05_vg_find.t: line 18: 1195140 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 16 x.vg t/05_vg_find.t: line 21: 1195147 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 16 x.vg t/05_vg_find.t: line 33: 1195163 Illegal instruction (core dumped) vg index -x m.xg inverting/m.vg rm: cannot remove 'm.xg': No such file or directory t/05_vg_find.t: line 38: 1195175 Illegal instruction (core dumped) vg construct -m 1000 -rmem/h.fa > h.vg t/05_vg_find.t: line 39: 1195176 Illegal instruction (core dumped) vg index -g h.gcsa -k 16 h.vg t/05_vg_find.t: line 43: 1195179 Illegal instruction (core dumped) vg construct -m 1000 -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 > giab.vg t/05_vg_find.t: line 44: 1195180 Illegal instruction (core dumped) vg index -x giab.xg -g giab.gcsa -k 11 giab.vg t/05_vg_find.t: line 61: 1195197 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/05_vg_find.t: line 62: 1195198 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 11 x.vg t/05_vg_find.t: line 63: 1195199 Illegal instruction (core dumped) vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam t/05_vg_find.t: line 65: 1195200 Illegal instruction (core dumped) vg gamsort -i x.sorted.gam.gai x.gam > x.sorted.gam t/05_vg_find.t: line 75: 1195220 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg t/05_vg_find.t: line 76: 1195221 Illegal instruction (core dumped) vg index -x tiny.xg tiny.vg t/05_vg_find.t: line 84: 1195233 Done echo '{"node": [{"id": 1, "sequence": "A"}, {"id": 2, "sequence": "A"}], "edge": [{"from": 1, "to": 2}], "path": [{"name": "ref", "mapping": [{"position": {"node_id": 1}}]}]}' 1195234 Illegal instruction (core dumped) | vg view -Jv - > test.vg t/05_vg_find.t: line 85: 1195235 Illegal instruction (core dumped) vg index -x test.xg test.vg t/05_vg_find.t: line 90: 1195241 Illegal instruction (core dumped) vg construct -m 1000 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a 2> /dev/null 1195242 (core dumped) | vg view -j - 1195243 Done | sed s/_alt/alt/g 1195244 (core dumped) | vg view -Jv - > w.vg t/05_vg_find.t: line 91: 1195245 Illegal instruction (core dumped) vg index -x w.xg w.vg t/05_vg_find.t: line 92: 1195246 Done cat w.vg 1195247 Illegal instruction (core dumped) | vg paths -d -v - > part1.tmp t/05_vg_find.t: line 93: 1195248 Illegal instruction (core dumped) vg find -x w.xg -Q alt > part2.tmp t/05_vg_find.t: line 97: 1195254 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg t/05_vg_find.t: line 98: 1195255 Illegal instruction (core dumped) vg index -x t.xg t.vg t/05_vg_find.t: line 101: 1195261 Illegal instruction (core dumped) vg find -x t.xg -E -p x:30-35 -p x:10-20 -W t. t/05_vg_find.t: line 102: 1195265 Illegal instruction (core dumped) vg view t.x:30:35.vg t/05_vg_find.t: line 102: 1195266 Illegal instruction (core dumped) vg view t.x:10:20.vg t/05_vg_find.t: line 106: 1195271 Illegal instruction (core dumped) vg find -x t.xg -E -R t.bed -W q. t/05_vg_find.t: line 107: 1195275 Illegal instruction (core dumped) vg view q.x:10:20.vg t/05_vg_find.t: line 107: 1195277 Illegal instruction (core dumped) vg view q.x:30:35.vg t/05_vg_find.t: line 107: 1195282 Illegal instruction (core dumped) vg view t.x:10:20.vg t/05_vg_find.t: line 107: 1195283 Illegal instruction (core dumped) vg view t.x:30:35.vg t/05_vg_find.t: line 113: 1195288 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/05_vg_find.t: line 114: 1195289 Illegal instruction (core dumped) vg index -x x.xg x.vg t/05_vg_find.t: line 115: 1195290 Illegal instruction (core dumped) vg index -G x.gbwt -v small/xy2.vcf.gz x.vg t/05_vg_find.t ........ 1..27 not ok 1 - construction # got: '132' # expected: '0' not ok 2 - unnamed test # got: '72' # expected: 'a path can be queried from the xg index' not ok 3 - a node near another can be obtained using context from the xg index # got: '0' # expected: '1' not ok 4 - each perfect read contains one maximal exact match # got: '0' # expected: '100' not ok 5 - unnamed test # got: '8' # expected: 'vg find -D finds approximate distance between 2 adjacent node starts' not ok 6 - unnamed test # got: '8' # expected: 'vg find -D finds approximate distance between node start and adjacent snp' not ok 7 - unnamed test # got: '7' # expected: 'vg find -D jumps deletion' not ok 8 - unnamed test # got: '7' # expected: 'vg find -D jumps deletion from other allele in snp' not ok 9 - vg find -L finds same number of nodes (with -c 1) # got: '0' # expected: '5' not ok 10 - vg find -L works with -r. it scans from start position of first node in range # got: '0' # expected: '3' not ok 11 - vg find -L tracks length from start position of input node # got: '0' # expected: '5' not ok 12 - vg find -L works with more than one input node # got: '0' # expected: '7' not ok 13 - unnamed test # got: '[["ACC",["1:-32"]],["CCGTTAG",["1:5"]],["GTTAGAGT",["1:19"]],["TAGAGTCAG",["1:40"]]]' # expected: 'we find the 4 canonical SMEMs from @lh3's bwa mem poster' not ok 14 - we can find the right MEMs for a sequence with Ns # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'f33b1420b5dc5126f5e74eecc6b79503' ok 15 - we find the same MEMs sequences with different lengths of Ns not ok 16 - the GAM index can return the set of alignments mapping to a node # got: '0' # expected: '6' not ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM # got: '0' # expected: '15' not ok 18 - the index can be queried using GAM alignments # got: '0' # expected: '1' not ok 19 - find gets connected edges between queried nodes by default # got: '0' # expected: '4' not ok 20 - find gets nodes provided in a node file list # got: '0' # expected: '4' not ok 21 - extracting by path adds no extra edges # got: '' # expected: '1' not ok 22 - pattern based path extraction works # got: '0' # expected: '38' not ok 23 - path DAG range query works # got: '0' # expected: '4' not ok 24 - we can extract a set of targets to separate files # got: '0' # expected: '20' ok 25 - the same extraction can be made using BED input not ok 26 - we see the expected number of kmers in the given targets # got: '0' # expected: '36' not ok 27 - unnamed test # got: '1510' # expected: 'we find the expected number of kmers with haplotype frequency equal to 2' Failed 25/27 subtests t/06_vg_index.t: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8): No such file or directory t/06_vg_index.t: line 13: 1195300 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/06_vg_index.t: line 15: 1195301 Illegal instruction (core dumped) vg index -x x.xg x.vg t/06_vg_index.t: line 18: 1195302 Illegal instruction (core dumped) vg index -g x.gcsa x.vg t/06_vg_index.t: line 21: 1195303 Illegal instruction (core dumped) vg index -x x2.xg -g x2.gcsa x.vg cmp: x.xg: No such file or directory t/06_vg_index.t: line 27: 1195305 Illegal instruction (core dumped) vg index -g x3.gcsa x.xg cmp: x.gcsa: No such file or directory t/06_vg_index.t: line 40: 1195311 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg t/06_vg_index.t: line 42: 1195312 Illegal instruction (core dumped) vg index -G x.gbwt -v small/x.vcf.gz x.vg t/06_vg_index.t: line 45: 1195313 Illegal instruction (core dumped) vg index -x x.xg x.vg t/06_vg_index.t: line 50: 1195317 Illegal instruction (core dumped) vg index -x x-ap.xg x.vg -L t/06_vg_index.t: line 55: 1195324 Illegal instruction (core dumped) vg index -g x.gcsa x.vg t/06_vg_index.t: line 58: 1195325 Illegal instruction (core dumped) vg index -x x2.xg -G x2.gbwt -v small/x.vcf.gz -g x2.gcsa x.vg cmp: x.xg: No such file or directory t/06_vg_index.t: line 64: 1195327 Illegal instruction (core dumped) vg index -x x2-ap.xg -G x2-ap.gbwt -v small/x.vcf.gz -g x2-ap.gcsa x.vg -L cmp: x.gbwt: No such file or directory t/06_vg_index.t: line 73: 1195335 Illegal instruction (core dumped) vg index -G empty.gbwt -v small/x.vcf.gz --exclude 1 x.vg t/06_vg_index.t: line 78: 1195337 Illegal instruction (core dumped) vg paths -v x.vg -X -Q _alt > x-alts.gam t/06_vg_index.t: line 79: 1195338 Illegal instruction (core dumped) vg index x.vg -M x-alts.gam -G x-gam.gbwt t/06_vg_index.t: line 81: 1195339 Illegal instruction (core dumped) vg convert x.vg -G x-alts.gam > x-alts.gaf t/06_vg_index.t: line 82: 1195340 Illegal instruction (core dumped) vg index x.vg -F x-alts.gaf -G x-gaf.gbwt cmp: x-gaf.gbwt: No such file or directory t/06_vg_index.t: line 95: 1195348 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a --region x:100-200 > x.part.vg t/06_vg_index.t: line 97: 1195349 Illegal instruction (core dumped) vg index -x x.part.xg -G x.part.gbwt --region x:100-200 -v small/x.vcf.gz x.part.vg 2> log.txt t/06_vg_index.t: line 106: 1195354 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C > x.vg 2> /dev/null t/06_vg_index.t: line 107: 1195355 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C > y.vg 2> /dev/null t/06_vg_index.t: line 108: 1195356 Illegal instruction (core dumped) vg ids -j x.vg y.vg t/06_vg_index.t: line 110: 1195357 Illegal instruction (core dumped) vg index -x xy.xg x.vg y.vg t/06_vg_index.t: line 113: 1195358 Illegal instruction (core dumped) vg index -g xy.gcsa -k 2 x.vg y.vg t/06_vg_index.t: line 116: 1195359 Illegal instruction (core dumped) vg index -x xy2.xg -g xy2.gcsa -k 2 x.vg y.vg cmp: xy.xg: No such file or directory t/06_vg_index.t: line 128: 1195364 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/06_vg_index.t: line 129: 1195365 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null t/06_vg_index.t: line 130: 1195366 Illegal instruction (core dumped) vg ids -j x.vg y.vg t/06_vg_index.t: line 132: 1195367 Illegal instruction (core dumped) vg index -G x.gbwt -v small/xy2.vcf.gz x.vg t/06_vg_index.t: line 135: 1195368 Illegal instruction (core dumped) vg index -x xy.xg x.vg y.vg t/06_vg_index.t: line 138: 1195369 Illegal instruction (core dumped) vg index -g xy.gcsa -k 2 x.vg y.vg t/06_vg_index.t: line 141: 1195370 Illegal instruction (core dumped) vg index -x xy2.xg -g xy2.gcsa -k 2 x.vg y.vg t/06_vg_index.t: line 144: 1195371 Illegal instruction (core dumped) vg index -x xy-alt.xg -L x.vg y.vg t/06_vg_index.t: line 147: 1195372 Illegal instruction (core dumped) vg index -G xy2.gbwt -v small/xy2.vcf.gz xy-alt.xg cmp: xy.xg: No such file or directory t/06_vg_index.t: line 161: 1195379 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/06_vg_index.t: line 163: 1195380 Illegal instruction (core dumped) vg index -G x_ref.gbwt -T x.vg t/06_vg_index.t: line 173: 1195382 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/06_vg_index.t: line 174: 1195383 Illegal instruction (core dumped) vg index -x x.xg x.vg bogus123.vg 2> /dev/null t/06_vg_index.t: line 177: 1195384 Illegal instruction (core dumped) vg kmers -k 16 -gB x.vg > x.graph t/06_vg_index.t: line 178: 1195385 Illegal instruction (core dumped) vg index -i x.graph -g x.gcsa t/06_vg_index.t: line 182: 1195387 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 11 x.vg t/06_vg_index.t: line 183: 1195390 Illegal instruction (core dumped) vg sim -n 100 -x x.xg t/06_vg_index.t: line 183: 1195389 Illegal instruction (core dumped) vg map -T <(vg sim -n 100 -x x.xg) -d x > x1337.gam t/06_vg_index.t: line 186: 1195391 Illegal instruction (core dumped) vg gamsort -i x1337.sorted.gam.gai2 x1337.gam > x1337.sorted.gam t/06_vg_index.t: line 187: 1195392 Illegal instruction (core dumped) vg index --index-sorted-gam x1337.sorted.gam t/06_vg_index.t: line 189: x1337.sorted.gam.gai: No such file or directory t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory t/06_vg_index.t: line 194: 1195398 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/06_vg_index.t: line 195: 1195399 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > y.vg t/06_vg_index.t: line 196: 1195400 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > z.vg t/06_vg_index.t: line 198: 1195401 Illegal instruction (core dumped) vg concat x.vg y.vg z.vg > q.vg t/06_vg_index.t: line 200: 1195402 Illegal instruction (core dumped) vg index -x q.xg q.vg t/06_vg_index.t: line 208: 1195405 Illegal instruction (core dumped) vg index -x r.xg reversing/reversing_x.vg t/06_vg_index.t: line 211: 1195406 Illegal instruction (core dumped) vg index -k 11 -g r.gcsa reversing/reversing_x.vg t/06_vg_index.t: line 233: 1195441 Illegal instruction (core dumped) vg construct -m 1025 -r 1mb1kgp/z.fa > big.vg t/06_vg_index.t: line 246: 1195451 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/06_vg_index.t: line 248: 1195452 Illegal instruction (core dumped) vg snarls -T x.vg > snarls.pb t/06_vg_index.t: line 251: 1195453 Illegal instruction (core dumped) vg index -s snarls.pb -j distIndex -w 100 x.vg t/06_vg_index.t: line 254: 1195454 Illegal instruction (core dumped) vg index -s snarls.pb -j distIndex x.vg t/06_vg_index.t ....... 1..51 not ok 1 - building an XG index of a graph # got: '132' # expected: '0' not ok 2 - building a GCSA index of a graph # got: '132' # expected: '0' not ok 3 - building both indexes at once # got: '132' # expected: '0' not ok 4 - the indexes are identical when built one at a time and together # got: '2' # expected: '0' not ok 5 - building GCSA from XG # got: '132' # expected: '0' not ok 6 - the GCSA indexes are identical when built from vg and from xg # got: '2' # expected: '0' not ok 7 - building a GBWT index of a graph with haplotypes # got: '132' # expected: '0' not ok 8 - building an XG index of a graph with haplotypes # got: '132' # expected: '0' not ok 9 - xg index does not contain alt paths by default # got: '0' # expected: '1' not ok 10 - building an XG index of a graph with haplotypes and alt paths included # got: '132' # expected: '0' ok 11 - xg index does contains alt paths with index -L not ok 12 - building a GCSA index of a graph with haplotypes # got: '132' # expected: '0' not ok 13 - building all indexes at once # got: '132' # expected: '0' not ok 14 - the indexes are identical # got: '2' # expected: '0' not ok 15 - building all indexes at once, while leaving alt paths in xg # got: '132' # expected: '0' not ok 16 - the indexes are identical with -L # got: '2' # expected: '0' ok 17 - xg index does contains alt paths with index -L all at once not ok 18 - samples can be excluded from haplotype indexing # got: '132' # expected: '0' not ok 19 - unnamed test # got: '0' # expected: 'excluded samples were not included in the GBWT index' not ok 20 - GBWT from GAF same as from GAM # got: '2' # expected: '0' not ok 21 - building GBWT index for a regional graph # got: '132' # expected: '0' ok 22 - no warnings about missing variants produced not ok 23 - building an XG index of multiple graphs # got: '132' # expected: '0' not ok 24 - building a GCSA index of multiple graphs # got: '132' # expected: '0' not ok 25 - building both indexes at once # got: '132' # expected: '0' not ok 26 - the indexes are identical # got: '2' # expected: '0' not ok 27 - building a GBWT index of multiple graphs with haplotypes # got: '132' # expected: '0' not ok 28 - building an XG index of multiple graphs with haplotypes # got: '132' # expected: '0' not ok 29 - building a GCSA index of multiple graphs with haplotypes # got: '132' # expected: '0' not ok 30 - building XG and GCSA indexes at once # got: '132' # expected: '0' not ok 31 - building an XG index with alt paths # got: '132' # expected: '0' not ok 32 - building a GBWT index from an XG index # got: '132' # expected: '0' not ok 33 - the indexes are identical # got: '2' # expected: '0' not ok 34 - GBWT can be built for paths # got: '132' # expected: '0' not ok 35 - fail with nonexistent file # got: '132' # expected: '1' not ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used # got: '132' # expected: '0' ok 37 - vg index and vg gamsort produce identical sorted GAM indexes not ok 38 - storage of multiple graphs in an index succeeds # got: '132' # expected: '0' not ok 39 - can index backward nodes # got: '132' # expected: '0' not ok 40 - can index kmers for backward nodes # got: '132' # expected: '0' not ok 41 - GCSA2 index works on cyclic graphs with heads and tails # got: '0' # expected: '1' not ok 42 - GCSA2 index works on cyclic graphs with no heads or tails # got: '0' # expected: '1' not ok 43 - GCSA2 index works on cyclic graphs with self loops # got: '0' # expected: '1' not ok 44 - GCSA2 index works on general cyclic graphs # got: '0' # expected: '1' not ok 45 - GCSA2 indexing of a tiny graph works # got: '0' # expected: '1' not ok 46 - GCSA2 indexing succeeds on a single-node graph # got: '0' # expected: '1' not ok 47 - GCSA2 indexing succeeds on graph with heads but no tails # got: '0' # expected: '1' not ok 48 - a useful error message is produced when nodes are too large # got: '0' # expected: '1' not ok 49 - snarl finding with trivial snarls # got: '132' # expected: '0' not ok 50 - building a distance index of a graph # got: '132' # expected: '0' not ok 51 - building a distance index of a graph without maximum index # got: '132' # expected: '0' Failed 47/51 subtests t/07_vg_map.t: line 10: 1195457 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/07_vg_map.t: line 11: 1195458 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 11 x.vg t/07_vg_map.t: line 35: 1195495 Illegal instruction (core dumped) vg map -s CTACTGACAGCAGAAGTTTGCTGTGAAGATTAAATTAGGTGATGCTTG -d x > /dev/null printf: usage: printf [-v var] format [arguments] t/07_vg_map.t: line 59: 1195543 Illegal instruction (core dumped) vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 > giab.vg t/07_vg_map.t: line 60: 1195544 Illegal instruction (core dumped) vg index -x giab.xg -g giab.gcsa -k 16 giab.vg t/07_vg_map.t: line 91: 1195589 Illegal instruction (core dumped) vg paths -d -v cyclic/orient_must_swap_edges.vg > e.vg t/07_vg_map.t: line 92: 1195590 Illegal instruction (core dumped) vg index -x e.xg -g e.gcsa -k 10 e.vg t/07_vg_map.t: line 93: 1195591 Illegal instruction (core dumped) vg map -s "ACACCTCCCTCCCGGACGGGGCGGCTGGCC" -d e > /dev/null t/07_vg_map.t: line 98: 1195593 Illegal instruction (core dumped) vg index -k10 -g g.idx.gcsa -x g.idx.xg graphs/multimap.vg t/07_vg_map.t: line 103: 1195599 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/07_vg_map.t: line 104: 1195600 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 16 x.vg t/07_vg_map.t: line 109: 1195610 Illegal instruction (core dumped) vg index -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -k 16 graphs/refonly-lrc_kir.vg t/07_vg_map.t: line 111: 1195611 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -u 4 -j > temp_paired_alignment.json t/07_vg_map.t: line 112: 1195612 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -u 4 -j > temp_independent_alignment.json t/07_vg_map.t: line 125: 1195645 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -j -t 1 --surject-to sam > temp_paired_alignment_xg.sam t/07_vg_map.t: line 126: 1195646 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -j -t 1 --surject-to sam > temp_paired_alignment_vg.sam t/07_vg_map.t: line 138: 1195658 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -u 4 -j t/07_vg_map.t: line 141: 1195659 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -i -u 4 -j t/07_vg_map.t: line 144: 1195660 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -f reads/NONEXISTENT -u 4 -j t/07_vg_map.t: line 147: 1195661 Illegal instruction (core dumped) vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -f reads/grch38_lrc_kir_paired.fq -u 4 -j t/07_vg_map.t: line 151: 1195662 Illegal instruction (core dumped) vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg t/07_vg_map.t: line 152: 1195663 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -v small/x.vcf.gz --gbwt-name x.gbwt -k 16 x.vg t/07_vg_map.t: line 163: 1195677 Illegal instruction vg map -d x -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG - ) --surject-to SAM > surjected.sam t/07_vg_map.t: line 163: 1195678 Illegal instruction (core dumped) vg view -a small/x-s13241-n1-p500-v300.gam 1195679 Done | sed 's%_1%/1%' 1195680 Done | sed 's%_2%/2%' 1195681 (core dumped) | vg view -JaG - t/07_vg_map.t: line 171: 1195714 Illegal instruction (core dumped) vg view -a small/x-s13241-n1-p500-v300.gam 1195715 Done | sed 's%_1%/1%' 1195716 Done | sed 's%_2%/2%' 1195717 (core dumped) | vg view -JaG - t/07_vg_map.t: line 171: 1195713 Illegal instruction (core dumped) vg map -d x -G <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG - ) --surject-to SAM > surjected.sam t/07_vg_map.t: line 180: 1195749 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg t/07_vg_map.t: line 181: 1195750 Illegal instruction (core dumped) vg index -k 16 -x tiny.xg -g tiny.gcsa tiny.vg t/07_vg_map.t: line 192: 1195759 Illegal instruction (core dumped) vg view -Fv graphs/revdrop.gfa > x.vg t/07_vg_map.t: line 193: 1195760 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa x.vg t/07_vg_map.t ......... 1..54 not ok 1 - offset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 2 - xdrop alignment obtains the expected result # got: '' # expected: '3' not ok 3 - xdrop alignment obtains the expected result for the reverse complement # got: '' # expected: '5' not ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 5 - offset counts unused bases from the start of the node on the reverse strand # got: '' # expected: '5' not ok 6 - global alignment traverses the correct path # got: '0' # expected: '4' not ok 7 - alignment score is as expected # got: '' # expected: '58' not ok 8 - scoring parameters are respected # got: '' # expected: '106' not ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected # got: '' # expected: '106' not ok 10 - full length bonus always be included # got: '' # expected: '58' not ok 11 - full length bonus can be set to 0 # got: '' # expected: '96' not ok 12 - vg map takes -d as input without a variant graph # got: '132' # expected: '0' not ok 13 - vg map can align across a SNP # got: '0' # expected: '1' not ok 14 - alignment works on a small graph # got: '0' # expected: '1000' ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities not ok 17 - chunky-banded alignment works # got: '0' # expected: '1' not ok 18 - unnamed test # got: '' # expected: 'multiple alignments are returned in descending score order' not ok 19 - only a single primary alignment is returned # got: '0' # expected: '1' not ok 20 - mapping of BAM file produces expected number of alignments # got: '0' # expected: '3333' not ok 21 - mapping from a fastq produces the expected number of alignments # got: '0' # expected: '3327' ok 22 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 23 - vg connects paired-end reads in gam output not ok 24 - mapping to graphs that can't be oriented without swapping edges works correctly # got: '132' # expected: '0' not ok 25 - reads multi-map to multiple possible locations # got: '0' # expected: '1' not ok 26 - vg map works based on gcsa and xg indexes # got: '0' # expected: '1000' not ok 27 - unnamed test # got: '30' # expected: 'the mapping quality may be capped' not ok 28 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 29 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 30 - only primary alignments have mapping quality scores # got: '0' # expected: '2' not ok 31 - unpaired reads produce mapping quality scores # got: '0' # expected: '1000' ok 32 - map returns same output on xg and vg (single threaded) not ok 33 - unnamed test # got: '10' # expected: 'base quality adjusted alignment produces higher scores if mismatches have low quality' not ok 34 - error on vg map -f (unpaired) # got: '132' # expected: '1' not ok 35 - error on vg map -f (interleaved) # got: '132' # expected: '1' not ok 36 - error on vg map -f (paired, LHS) # got: '132' # expected: '1' not ok 37 - error on vg map -f (paired, RHS) # got: '132' # expected: '1' not ok 38 - mapping a read that touches unused nodes gets the base score # got: '' # expected: '36' not ok 39 - mapping a read that matches a haplotype gets a small penalty # got: '' # expected: '35' not ok 40 - mapping a read that matches a haplotype with exponent 0 gets the base score # got: '' # expected: '36' not ok 41 - mapping a read that matches no haplotypes gets a larger penalty # got: '' # expected: '21' not ok 42 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 43 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 44 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 45 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 46 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 47 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 48 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 49 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 50 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 51 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' not ok 52 - unnamed test # got: '1' # expected: 'mapper can read FASTA input' not ok 53 - unnamed test # got: '1' # expected: 'mapper can read multiline FASTA input' not ok 54 - unnamed test # got: '130' # expected: 'xdrop works on a reversed read' Failed 49/54 subtests t/08_vg_ids.t: line 16: 1195790 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/08_vg_ids.t: line 17: 1195791 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > y.vg t/08_vg_ids.t: line 18: 1195792 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > z.vg t/08_vg_ids.t: line 20: 1195793 Illegal instruction (core dumped) vg ids -j x.vg y.vg z.vg (standard_in) 1: syntax error t/08_vg_ids.t: line 29: 1195810 Illegal instruction (core dumped) vg ids -s cyclic/self_loops.vg > sorted.vg t/08_vg_ids.t: line 32: 1195811 Illegal instruction (core dumped) vg ids -s cyclic/all.vg > sorted.vg t/08_vg_ids.t ......... 1..10 not ok 1 - unnamed test # got: '1' # expected: 'minimum node as expected (id compaction correct)' not ok 2 - unnamed test # got: '0' # expected: 'maximum node is as expected (id compaction correct)' not ok 3 - unnamed test # got: 'correctly generated joint id space for several graphs' # expected: '' not ok 4 - can sort and re-number a graph with self loops # got: '132' # expected: '0' not ok 5 - can sort and renumber a complex cyclic graph # got: '132' # expected: '0' ok 6 - sorting removes back-edges in a DAG not ok 7 - unnamed test # got: 'true' # expected: 'sorting assigns node IDs in topological order' not ok 8 - unnamed test # got: 'sorting does not affect id range' # expected: '' not ok 9 - unnamed test # got: 'sorting does not affect id range of vg' # expected: '' not ok 10 - unnamed test # got: 'sorting does not affect id range of hg' # expected: '' Failed 9/10 subtests t/09_vg_concat.t: line 10: 1195846 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/09_vg_concat.t: line 22: 1195872 Illegal instruction (core dumped) vg view -Jv ./reversing/reversing_path.json > reversing.vg t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes not ok 2 - concat doubles the number of edges + 1 # got: '0' # expected: '1' ok 3 - concat -p doubles the number of nodes on reversing graph not ok 4 - concat -p doubles the number of edges + 1 on reversing graph # got: '0' # expected: '1' Failed 2/4 subtests t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok t/10_vg_stats.t: line 10: 1195905 Illegal instruction (core dumped) vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg t/10_vg_stats.t: line 33: 1195939 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg t/10_vg_stats.t: line 38: 1195947 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -a -f -v small/x.vcf.gz > x.vg t/10_vg_stats.t: line 39: 1195948 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 16 x.vg t/10_vg_stats.t: line 40: 1195949 Illegal instruction (core dumped) vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam t/10_vg_stats.t: line 48: 1195963 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa 1195964 Illegal instruction (core dumped) | vg view -g - > tiny_names.gfa t/10_vg_stats.t: line 51: 1195965 Illegal instruction (core dumped) vg view -Fv tiny_names.gfa > tiny_names.vg t/10_vg_stats.t: line 56: 1195971 Illegal instruction (core dumped) vg convert graphs/atgc.vg -v > atgc.vg t/10_vg_stats.t: line 58: 1195973 Illegal instruction (core dumped) vg convert graphs/atgc.vg -a > atgc.hg t/10_vg_stats.t: line 60: 1195975 Illegal instruction (core dumped) vg convert graphs/atgc.vg -p > atgc.pg t/10_vg_stats.t: line 62: 1195977 Illegal instruction (core dumped) vg convert graphs/atgc.vg -o > atgc.og t/10_vg_stats.t: line 64: 1195979 Illegal instruction (core dumped) vg index graphs/atgc.vg -x atgc.xg t/10_vg_stats.t ....... 1..18 not ok 1 - unnamed test # got: '0' # expected: 'vg stats reports the expected number of nodes' not ok 2 - unnamed test # got: '0' # expected: 'vg stats reports the expected number of edges' not ok 3 - unnamed test # got: '0' # expected: 'vg stats reports the expected graph length' not ok 4 - vg stats reports the correct number of subgraphs # got: '0' # expected: '1' not ok 5 - unnamed test # got: 'vg stats reports the correct subgraph length' # expected: '' not ok 6 - unnamed test # got: '38' # expected: 'distance to head is correct' not ok 7 - unnamed test # got: '11' # expected: 'distance to tail is correct' not ok 8 - aligned read stats are computed correctly # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'b45c940480441a36475217a41b35e1f6' ok 9 - basic stats agree between graph formats not ok 10 - stats can be computed for GAM files without graphs # got: '' # expected: 'Total alignments: 100' not ok 11 - a path overlap description of a test graph has the expected length # got: '0' # expected: '113' not ok 12 - vg stats -F detects format of old protobuf graph # got: '' # expected: 'format: VG-Protobuf' not ok 13 - vg stats -F detects format of newer protobuf graph # got: '' # expected: 'format: VG-Protobuf' not ok 14 - vg stats -F detects format of hash graph # got: '' # expected: 'format: HashGraph' not ok 15 - vg stats -F detects format of packed graph # got: '' # expected: 'format: PackedGraph' not ok 16 - vg stats -F detects format of odgi graph # got: '' # expected: 'format: ODGI' not ok 17 - vg stats -F detects format of xg graph # got: '' # expected: 'format: XG' 0a1 > 2 12 3 9 8 not ok 18 - vg stats -D found correct degree distribution of tiny graph # got: '1' # expected: '0' Failed 17/18 subtests t/11_vg_paths.t: line 12: 1195989 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg t/11_vg_paths.t: line 13: 1195990 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x2.vg t/11_vg_paths.t: line 14: 1195991 Illegal instruction (core dumped) vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg t/11_vg_paths.t: line 33: 1196013 Illegal instruction (core dumped) vg paths -x x.xg -Q x -F > x_from_xg.fa t/11_vg_paths.t: line 36: 1196015 Illegal instruction (core dumped) vg paths -v x.vg -Q x -F > x_from_vg.fa t/11_vg_paths.t ....... 1..14 not ok 1 - path listing works from vg # got: '' # expected: 'x' not ok 2 - path listing works from XG # got: '' # expected: 'x' not ok 3 - thread listing works from GBWT # got: '0' # expected: '2' not ok 4 - thread selection by name prefix works correctly # got: '0' # expected: '1' not ok 5 - thread selection by sample name works correctly # got: '0' # expected: '2' ok 6 - no threads are reported for invalid samples not ok 7 - vg paths may be used to extract threads # got: '0' # expected: '2' not ok 8 - vg paths may be used to extract threads as GAF # got: '0' # expected: '2' 0a1,14 > >x > CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG > TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA > TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG > TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT > ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT > TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT > CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG > CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT > TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC > TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG > CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT > TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA not ok 9 - Fasta extracted from xg is the same as the input fasta # got: '1' # expected: '0' 0a1,14 > >x > CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG > TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA > TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG > TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT > ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT > TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT > CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG > CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT > TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC > TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG > CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT > TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA not ok 10 - Fasta extracted from vg is the same as the input fasta # got: '1' # expected: '0' not ok 11 - Fasta extracted from threads has correct number of lines # got: '0' # expected: '28' not ok 12 - a single path may be retained # got: '0' # expected: '1' ok 13 - path filtering does not modify the graph not ok 14 - alt allele paths can be dropped # got: '0' # expected: '1' Failed 12/14 subtests t/12_vg_kmers.t: line 20: 1196064 Illegal instruction (core dumped) vg construct -v small/x.vcf.gz -r small/x.fa > x.vg t/12_vg_kmers.t: line 35: 1196082 Illegal instruction (core dumped) vg mod -p -l 11 -e 8 -S jumble/j.vg > j.vg t/12_vg_kmers.t: line 44: 1196092 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa 1196093 (core dumped) | vg view - 1196094 Done | head -10 1196095 (core dumped) | vg view -vF - 1196096 (core dumped) | vg mod -o - 1196097 (core dumped) | vg kmers -k 16 - > /dev/null t/12_vg_kmers.t ....... 1..10 not ok 1 - correct numbers of kmers in the graph # got: '0' # expected: '4250' not ok 2 - to_end edges are handled correctly # got: '0' # expected: '1' not ok 3 - from_start edges are handled correctly # got: '0' # expected: '1' not ok 4 - GCSA2 output produces the expected number of lines # got: '0' # expected: '4356' not ok 5 - GCSA2 binary output produces the expected number bytes # got: '0' # expected: '111528' not ok 6 - GCSA2 output works when next position is multiple # got: '' # expected: 'A,G 7:0,8:0' not ok 7 - GCSA2 output works when previous characters are multiple # got: '' # expected: 'G,A' not ok 8 - edge-max correctly bounds the number of kmers in a complex graph # got: '0' # expected: '26148' not ok 9 - start/stop node IDs can be specified in GCSA2 output # got: '0' # expected: '76' not ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers # got: '132' # expected: '0' Failed 10/10 subtests t/13_vg_sim.t: line 11: 1196099 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/13_vg_sim.t: line 12: 1196100 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a > x2.vg t/13_vg_sim.t: line 13: 1196101 Illegal instruction (core dumped) vg index -x x.xg x.vg t/13_vg_sim.t: line 14: 1196102 Illegal instruction (core dumped) vg index -G x.gbwt -v small/x.vcf.gz x2.vg t/13_vg_sim.t: line 36: 1196143 Illegal instruction (core dumped) vg sim -n 100 -l 100 -A -x x.xg -r > reads.txt 2> log.txt t/13_vg_sim.t: line 40: 1196145 Illegal instruction (core dumped) vg sim -n 100 -l 100 -m 1 -g x.gbwt -x x.xg -r > reads.txt 2> log.txt t/13_vg_sim.t: line 49: 1196153 Illegal instruction (core dumped) vg construct -r n.fa > n.vg t/13_vg_sim.t: line 50: 1196154 Illegal instruction (core dumped) vg index -x n.xg n.vg t/13_vg_sim.t: line 59: 1196169 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/x.vcf.gz -a > xy.vg t/13_vg_sim.t: line 60: 1196170 Illegal instruction (core dumped) vg index -x xy.xg xy.vg t/13_vg_sim.t: line 61: 1196171 Illegal instruction (core dumped) vg index -G xy.gbwt -v small/x.vcf.gz xy.vg t/13_vg_sim.t: line 63: 1196172 Illegal instruction (core dumped) vg sim -s 12345 -n 1000 -l 2 -e 0.1 -x xy.xg -g xy.gbwt --sample-name 1 --any-path > /dev/null t/13_vg_sim.t: line 74: 1196217 Illegal instruction (core dumped) vg sim -s 12345 -n 1000 -l 2 -e 0.1 -x xy.xg -g xy.gbwt --sample-name 1 --any-path -F minigiab/NA12878.chr22.tiny.fq.gz > /dev/null t/13_vg_sim.t: line 87: 1196263 Illegal instruction (core dumped) vg view -Fv graphs/cactus-BRCA2.gfa > cactus-BRCA2.vg t/13_vg_sim.t: line 88: 1196264 Illegal instruction (core dumped) vg index -x cactus-BRCA2.xg cactus-BRCA2.vg t/13_vg_sim.t ......... 1..34 not ok 1 - vg sim creates the correct number of reads # got: '0' # expected: '100' not ok 2 - unnamed test # got: '110' # expected: 'end bonuses are included' not ok 3 - alignments may be generated rather than read sequences # got: '0' # expected: '100' not ok 4 - alignments are produced on both strands # got: '0' # expected: '1' not ok 5 - high simulated error rates do not change the number of bases generated # got: '0' # expected: '10300' ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode not ok 9 - reads can be simulated from all paths # got: '132' # expected: '0' not ok 10 - simulation was successful # got: '0' # expected: '1' not ok 11 - reads can be simulated from GBWT samples # got: '132' # expected: '0' not ok 12 - simulation was successful # got: '0' # expected: '1' not ok 13 - pairs simulated even when fragments overlap # got: '0' # expected: '20' ok 14 - sim does not emit reads with Ns not ok 15 - sim can emit reads with Ns when asked to # got: '0' # expected: '1' ok 16 - sim doesn't emit Ns even with pair and errors not ok 17 - Sample simulation works along with --any-path # got: '132' # expected: '0' not ok 18 - not having any regexes skips all unvisited contigs # got: '0' # expected: '1000' not ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs # got: '0' # expected: '1' not ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs # got: '0' # expected: '1' not ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig # got: '0' # expected: '1000' not ok 22 - multiple regexes are interpreted # got: '0' # expected: '1000' not ok 23 - regexes are interpreted as regexes # got: '0' # expected: '1000' not ok 24 - assigning a very high ploidy by regex starves out the other paths # got: '0' # expected: '1000' not ok 25 - Sample simulation works along with --any-path with training FASTQ # got: '132' # expected: '0' not ok 26 - not having any regexes skips all unvisited contigs with training FASTQ # got: '0' # expected: '1000' not ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ # got: '0' # expected: '1' not ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ # got: '0' # expected: '1' not ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ # got: '0' # expected: '1000' not ok 30 - multiple regexes are interpreted with training FASTQ # got: '0' # expected: '1000' not ok 31 - regexes are interpreted as regexes with training FASTQ # got: '0' # expected: '1000' not ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ # got: '0' # expected: '1000' not ok 33 - ngs trained simulator works # got: '0' # expected: '100' not ok 34 - ngs trained simulator generates gam # got: '0' # expected: '200' Failed 29/34 subtests t/14_vg_mod.t: line 26: 1196313 Illegal instruction (core dumped) vg mod -n msgas/q_redundant.vg 1196314 (core dumped) | vg validate - t/14_vg_mod.t: line 29: 1196315 Illegal instruction vg mod -U 10 msgas/q_redundant.vg 1196316 Illegal instruction (core dumped) | vg validate - t/14_vg_mod.t: line 32: 1196317 Illegal instruction (core dumped) vg mod -u msgas/q_redundant.vg 1196318 Illegal instruction | vg validate - t/14_vg_mod.t: line 46: 1196347 Illegal instruction vg view -Jv reversing/reversing_path.json 1196348 Illegal instruction (core dumped) | vg mod -X 3 - 1196349 Illegal instruction (core dumped) | vg validate - t/14_vg_mod.t: line 58: 1196369 Illegal instruction (core dumped) vg msga -w 20 -f msgas/s.fa > s.vg t/14_vg_mod.t: line 59: 1196370 Illegal instruction (core dumped) vg msga -g s.vg -s TCAGATTCTCATCCCTCCTCAAGGGCTTCTGTAGCTTTGATGTGGAGTAGTTCCAGGCCATTTTAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAG -w 16 -N > s2.vg t/14_vg_mod.t: line 60: 1196371 Illegal instruction (core dumped) vg mod -u s2.vg > /dev/null t/14_vg_mod.t: line 64: 1196373 Illegal instruction (core dumped) vg msga -f msgas/l.fa -b a1 -w 16 1196374 (core dumped) | vg mod -X 8 - 1196375 (core dumped) | vg validate - t/14_vg_mod.t: line 67: 1196376 Illegal instruction (core dumped) vg mod -U 3 graphs/atgclinv2.vg 1196377 (core dumped) | vg validate - t/14_vg_mod.t: line 70: 1196378 Illegal instruction vg mod -U 3 graphs/atgclinv2.vg 1196379 Illegal instruction (core dumped) | vg mod -f 50 - 1196380 Illegal instruction (core dumped) | vg validate - t/14_vg_mod.t: line 77: 1196437 Illegal instruction (core dumped) vg mod -f 6 graphs/atgclinv2.vg 1196438 Illegal instruction | vg mod -d 5 - 1196439 (core dumped) | vg validate - t/14_vg_mod.t: line 84: 1196478 Illegal instruction (core dumped) vg mod -w 100 graphs/ununrollable.vg 1196479 (core dumped) | vg validate - t/14_vg_mod.t: line 87: 1196480 Illegal instruction (core dumped) vg mod -s graphs/not-simple.vg 1196481 (core dumped) | vg validate - t/14_vg_mod.t: line 90: 1196482 Illegal instruction vg msga -g <(vg msga -f msgas/cycle.fa -b s1 -w 19 -O 18 -k 4 -t 1 | vg paths -d -v - | vg mod -U 10 -) -f msgas/cycle.fa -t 1 1196483 Illegal instruction (core dumped) | vg mod -N - 1196484 Illegal instruction (core dumped) | vg paths -d -v - 1196486 Illegal instruction (core dumped) | vg mod -U 10 - > c.vg t/14_vg_mod.t: line 90: 1196487 Illegal instruction (core dumped) vg msga -f msgas/cycle.fa -b s1 -w 19 -O 18 -k 4 -t 1 1196488 (core dumped) | vg paths -d -v - 1196489 (core dumped) | vg mod -U 10 - t/14_vg_mod.t: line 96: 1196500 Illegal instruction (core dumped) vg construct -r small/x.fa -a -f -v small/x.vcf.gz > x.vg t/14_vg_mod.t: line 97: 1196501 Illegal instruction (core dumped) vg mod -v small/x.vcf.gz x.vg > x.sample.vg t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path not ok 2 - orphan edge removal is automatic # got: '0' # expected: '8' not ok 3 - unnamed test # got: '285' # expected: 'graph complexity reduction works as expected' not ok 4 - unnamed test # got: '983' # expected: 'short subgraph pruning works' not ok 5 - normalization produces the correct number of nodes # got: '0' # expected: '4' not ok 6 - normalization removes redundant SNP alleles # got: '0' # expected: '4' not ok 7 - normalization produces a valid graph # got: '132' # expected: '0' not ok 8 - looped normalization produces a valid graph # got: '132' # expected: '0' not ok 9 - unchop produces a valid graph # got: '132' # expected: '0' not ok 10 - unnamed test # got: '154' # expected: 'normalization removes redundant sequence in the graph' not ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '5d3999dfcafb09801e4659c1b43a8593' ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '132' # expected: '0' not ok 14 - unnamed test # got: '2f785068c91dbe84177c1fd679b6f133' # expected: 'unchop correctly handles paths' ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion not ok 18 - mod successfully unchops a difficult graph # got: '132' # expected: '0' not ok 19 - chopping self-cycling nodes retains the cycle # got: '132' # expected: '0' not ok 20 - unrolling works and produces a valid graph # got: '132' # expected: '0' not ok 21 - unfolding works and produces a valid graph # got: '132' # expected: '0' ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph not ok 24 - dagify handles a graph with two strongly connected components # got: '132' # expected: '0' not ok 25 - unnamed test # got: '0' # expected: 'unfold followed by dagify produces a graph with no cycles' ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph not ok 27 - dagify unrolls the un-unrollable graph # got: '132' # expected: '0' not ok 28 - sibling simplification does not disrupt paths # got: '132' # expected: '0' not ok 29 - unnamed test # got: '4' # expected: 'dagify correctly calculates the minimum distance through the unrolled component' not ok 30 - unnamed test # got: '200' # expected: 'dagify produces a graph of the correct size' not ok 31 - unnamed test # got: '1041' # expected: 'subsetting a flat-alleles graph to a sample graph works' not ok 32 - removal of high-degree nodes results in the expected number of subgraphs # got: '0' # expected: '7' Failed 25/32 subtests t/15_vg_surject.t: line 11: 1196511 Illegal instruction (core dumped) vg construct -r small/x.fa > j.vg t/15_vg_surject.t: line 12: 1196512 Illegal instruction (core dumped) vg index -x j.xg j.vg t/15_vg_surject.t: line 13: 1196513 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/15_vg_surject.t: line 14: 1196514 Illegal instruction (core dumped) vg index -k 11 -g x.gcsa -x x.xg x.vg t/15_vg_surject.t: line 17: 1196515 Illegal instruction (core dumped) vg map -G small/x-allref-nohptrouble.gam -g x.gcsa -x x.xg > j.gam t/15_vg_surject.t: line 19: 1196517 Illegal instruction (core dumped) vg map -G <(vg sim -a -n 100 -x x.xg) -g x.gcsa -x x.xg > x.gam t/15_vg_surject.t: line 19: 1196518 Illegal instruction (core dumped) vg sim -a -n 100 -x x.xg [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 72: 1196590 Illegal instruction (core dumped) vg map -f fwd.fq -g x.gcsa -x x.xg > mapped.fwd.gam t/15_vg_surject.t: line 73: 1196591 Illegal instruction (core dumped) vg map -f rev.fq -g x.gcsa -x x.xg > mapped.rev.gam [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 87: 1196619 Done echo '{"sequence": "CAAATAA", "path": {"mapping": [{"position": {"node_id": 1}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "mapping_quality": 99}' 1196620 Illegal instruction (core dumped) | vg view -JGa - > read.gam t/15_vg_surject.t: line 90: 1196625 Done echo '{"name": "read/2", "sequence": "CAAATAA", "path": {"mapping": [{"position": {"node_id": 1}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "fragment_prev": {"name": "read/1"}}{"name": "read/1", "sequence": "CTTATTT", "path": {"mapping": [{"position": {"node_id": 1, "is_reverse": true}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "fragment_next": {"name": "read/2"}}' 1196626 Illegal instruction (core dumped) | vg view -JGa - > read.gam t/15_vg_surject.t: line 93: 1196631 Illegal instruction (core dumped) vg surject -p x -x x.xg -i read.gam -s > read.gam.surject.sam t/15_vg_surject.t: line 94: 1196632 Illegal instruction vg convert x.xg -G read.gam -t 1 1196633 Illegal instruction (core dumped) | vg surject -p x -x x.xg -i -G - -s > read.gaf.surject.sam t/15_vg_surject.t: line 99: 1196636 Illegal instruction (core dumped) vg map -d x -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG - ) 1196637 (core dumped) | vg surject -x x.xg -p x -s -i -N Sample1 -R RG1 - > surjected.sam t/15_vg_surject.t: line 99: 1196639 Illegal instruction (core dumped) vg view -a small/x-s13241-n1-p500-v300.gam 1196640 Done | sed 's%_1%/1%' 1196641 Done | sed 's%_2%/2%' 1196642 (core dumped) | vg view -JaG - t/15_vg_surject.t: line 110: 1196685 Illegal instruction (core dumped) vg mod -c graphs/fail.vg > f.vg t/15_vg_surject.t: line 111: 1196686 Illegal instruction (core dumped) vg index -k 11 -g f.gcsa -x f.xg f.vg t/15_vg_surject.t: line 119: 1196693 Illegal instruction (core dumped) vg mod -c graphs/fail2.vg > f.vg t/15_vg_surject.t: line 120: 1196694 Illegal instruction (core dumped) vg index -k 11 -g f.gcsa -x f.xg f.vg t/15_vg_surject.t: line 127: 1196701 Illegal instruction (core dumped) vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz > minigiab.vg t/15_vg_surject.t: line 128: 1196702 Illegal instruction (core dumped) vg index -k 11 -g m.gcsa -x m.xg minigiab.vg [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". t/15_vg_surject.t ..... 1..33 not ok 1 - reads are generated # got: '0' # expected: '100' not ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 4 - vg surject actually places reads on the correct path # got: '0' # expected: '100' not ok 5 - vg surject doesn't need to be told which path to use # got: '0' # expected: '100' not ok 6 - vg surject works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 7 - vg surject spliced algorithm works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 8 - vg surject produces valid SAM output # got: '0' # expected: '100' not ok 9 - vg map may surject reads to produce valid SAM output # got: '0' # expected: '100' not ok 10 - vg map may surject reads to produce valid BAM output # got: '0' # expected: '100' not ok 11 - vg surject retains read names # got: '0' # expected: '100' not ok 12 - vg surject can set sample and read group # got: '0' # expected: '100' not ok 13 - we respect the original mapping's softclips # got: '0' # expected: '1' ok 14 - quality strings we will use for testing are oriented correctly ok 15 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags not ok 16 - vg surject produces valid BAM output # got: '0' # expected: '100' not ok 17 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 18 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' ok 19 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 25 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 26 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' not ok 27 - surjection works for a longer (151bp) read # got: '0' # expected: '1' not ok 28 - surjection works for another difficult read # got: '0' # expected: '1' not ok 29 - mapping reproduces qualities from BAM input # got: '0' # expected: '1' not ok 30 - mapping reproduces qualities from fastq input # got: '0' # expected: '1' not ok 31 - mapping reproduces qualities from GAF input # got: '0' # expected: '1' not ok 32 - surject works on GAMP input # got: '0' # expected: '1000' not ok 33 - surject works on paired GAMP input # got: '0' # expected: '1000' Failed 30/33 subtests t/16_vg_msga.t: line 24: 1196757 Illegal instruction (core dumped) vg msga -f msgas/s.fa -w 16 1196758 (core dumped) | vg mod -U 10 - 1196759 (core dumped) | vg mod -c - 1196760 (core dumped) | vg view -j - t/16_vg_msga.t: line 28: 1196761 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > t.vg t/16_vg_msga.t: line 34: 1196791 Illegal instruction (core dumped) vg msga -f msgas/s.fa -b s1 -w 20 -O 10 1196792 (core dumped) | vg mod -U 10 - 1196793 (core dumped) | vg mod -c - > s.vg t/16_vg_msga.t: line 35: 1196794 Illegal instruction (core dumped) vg msga -g s.vg -f msgas/s-rev.fa -w 20 -O 10 1196795 (core dumped) | vg mod -U 10 - 1196796 (core dumped) | vg mod -c - > s+rev.vg t/16_vg_msga.t: line 41: 1196821 Illegal instruction vg msga -f msgas/w.fa -b x -K 16 -w 20 1196822 Illegal instruction (core dumped) | vg validate - t/16_vg_msga.t: line 44: 1196823 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/K-3138.fa -w 256 -W 64 -E 4 1196824 Illegal instruction (core dumped) | vg validate - t/16_vg_msga.t: line 47: 1196825 Illegal instruction (core dumped) vg msga -f msgas/cycle.fa -b s1 -w 64 -t 1 1196826 (core dumped) | vg validate - t/16_vg_msga.t: line 52: 1196833 Illegal instruction (core dumped) vg msga -f msgas/l.fa -b a1 -w 16 1196834 (core dumped) | vg validate - t/16_vg_msga.t: line 55: 1196835 Illegal instruction (core dumped) vg msga -f GRCh38_alts/FASTA/HLA/B-3106.fa -w 256 -E 4 -B 4 -W 64 -P 0.9 1196836 (core dumped) | vg validate - t/16_vg_msga.t: line 58: 1196837 Illegal instruction (core dumped) vg msga -f msgas/inv.fa -w 16 -O 5 1196838 Illegal instruction | vg validate - t/16_vg_msga.t ........ 1..14 not ok 1 - MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '16e56f0090b310d2b1479d49cf790324' not ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '2ab075dd73c31ea9939726d72c12655f' not ok 3 - soft clips at node boundaries (start) are included correctly # got: '0' # expected: '1' not ok 4 - soft clips at node boundaries (end) are included correctly # got: '0' # expected: '1' ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph not ok 7 - the paths of the graph encode the original sequences used to build it # got: '0' # expected: '2' not ok 8 - even when banding the paths of the graph encode the original sequences used to build it # got: '132' # expected: '0' not ok 9 - HLA K-3138 correctly includes all input paths # got: '132' # expected: '0' not ok 10 - a difficult cyclic path can be included to produce a valid graph # got: '132' # expected: '0' not ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected # got: '0' # expected: '1' not ok 12 - edges in cycles with two nodes are correctly included # got: '132' # expected: '0' not ok 13 - HLA B-3106 is assembled into a valid graph # got: '132' # expected: '0' not ok 14 - odd-sized overlaps may be used for chunked alignment # got: '132' # expected: '0' Failed 12/14 subtests t/17_vg_augment.t: line 11: 1196840 Illegal instruction (core dumped) vg view -J -v pileup/tiny.json > tiny.vg t/17_vg_augment.t: line 14: 1196841 Illegal instruction (core dumped) vg view -J -a -G pileup/edits.json > edits.gam t/17_vg_augment.t: line 15: 1196842 Illegal instruction (core dumped) vg augment -a direct tiny.vg edits.gam -A edits-embedded.gam > augmented.vg t/17_vg_augment.t: line 22: 1196849 Illegal instruction (core dumped) vg augment -a direct tiny.vg edits.gam -A edits-embedded.gam -m 1 > augmented.m1.vg t/17_vg_augment.t: line 26: 1196851 Illegal instruction (core dumped) vg convert tiny.vg -G edits.gam > edits.gaf t/17_vg_augment.t: line 27: 1196852 Illegal instruction (core dumped) vg augment -a direct tiny.vg edits.gaf -F -A edits-embedded.gaf > augmented.gaf.vg t/17_vg_augment.t: line 28: 1196853 Illegal instruction (core dumped) vg convert augmented.gaf.vg -F edits-embedded.gaf > edits-embedded.gaf.gam t/17_vg_augment.t: line 35: 1196861 Illegal instruction (core dumped) vg view -J -a -G pileup/edit.json > edit.gam t/17_vg_augment.t: line 36: 1196862 Illegal instruction (core dumped) vg augment -a direct tiny.vg edit.gam -A edit-embedded.gam > augmented.vg t/17_vg_augment.t: line 48: 1196871 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa > t.vg t/17_vg_augment.t: line 49: 1196872 Illegal instruction (core dumped) vg index -k 11 -g t.idx.gcsa -x t.idx.xg t.vg t/17_vg_augment.t: line 69: 1196919 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > t.vg t/17_vg_augment.t: line 70: 1196920 Illegal instruction (core dumped) vg align -s GGGGGGGAAATTTTCTGGAGTTCTATTATATTCCAAAAAAAAAA t.vg > t.gam Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. t/17_vg_augment.t: line 73: 1196941 Illegal instruction (core dumped) vg align -s AAATTTTCTGGAGTTCTAT t.vg >> t.gam t/17_vg_augment.t: line 74: 1196942 Illegal instruction (core dumped) vg find -x t.vg -n 9 -c 1 > n9.vg t/17_vg_augment.t: line 75: 1196943 Illegal instruction (core dumped) vg augment n9.vg t.gam -s -A n9_aug.gam > /dev/null t/17_vg_augment.t: line 79: 1196948 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/17_vg_augment.t: line 80: 1196949 Illegal instruction (core dumped) vg index -x x.xg -g x.gcsa -k 16 x.vg t/17_vg_augment.t: line 81: 1196950 Illegal instruction (core dumped) vg map -x x.xg -g x.gcsa -G small/x-s1337-n100-e0.01-i0.005.gam -t 1 > x.gam t/17_vg_augment.t: line 82: 1196951 Illegal instruction (core dumped) vg augment -Z x.trans -i -S x.vg x.gam > x.mod.vg t/17_vg_augment.t: line 86: 1196956 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa > flat.vg t/17_vg_augment.t: line 87: 1196957 Illegal instruction (core dumped) vg view flat.vg 1196958 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' 1196959 (core dumped) | vg view -Fv - > 2snp.vg t/17_vg_augment.t: line 88: 1196960 Illegal instruction (core dumped) vg index -x 2snp.xg 2snp.vg t/17_vg_augment.t: line 89: 1196961 Illegal instruction (core dumped) vg sim -l 30 -x 2snp.xg -n 30 -a > 2snp.sim t/17_vg_augment.t: line 90: 1196962 Illegal instruction (core dumped) vg index -x flat.xg -g flat.gcsa -k 16 flat.vg t/17_vg_augment.t: line 91: 1196963 Illegal instruction (core dumped) vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam t/17_vg_augment.t: line 94: 1196971 Illegal instruction (core dumped) vg view flat.vg 1196972 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTATCTGGAGTTCTATTATATCCCAACTCTCTG/' 1196973 (core dumped) | vg view -Fv - > 2err.vg t/17_vg_augment.t: line 95: 1196974 Illegal instruction (core dumped) vg sim -l 30 -x 2err.vg -n 10 -a > 2err.sim t/17_vg_augment.t: line 96: 1196975 Illegal instruction (core dumped) vg map -g flat.gcsa -x flat.xg -G 2err.sim -k 8 > 2err.gam t/17_vg_augment.t: line 116: 1196994 Illegal instruction (core dumped) vg map -g flat.gcsa -x flat.xg -f qual.fq -k 8 > 2qual.gam t/17_vg_augment.t: line 123: 1197010 Illegal instruction (core dumped) vg convert flat.vg -p > flat.pg t/17_vg_augment.t: line 127: 1197018 Illegal instruction (core dumped) vg convert flat.vg -a > flat.hg t/17_vg_augment.t: line 135: 1197028 Illegal instruction (core dumped) vg construct -m 10 -r tiny/tiny.fa > t.vg t/17_vg_augment.t: line 136: 1197029 Illegal instruction (core dumped) vg index -k 11 -g t.idx.gcsa -x t.idx.xg t.vg t/17_vg_augment.t: line 140: 1197039 Illegal instruction (core dumped) vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197040 Illegal instruction | vg augment t.vg - -N 1 -m 0 > t.aug1.vg t/17_vg_augment.t: line 145: 1197046 Illegal instruction vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197047 Illegal instruction (core dumped) | vg augment t.vg - -N 0.5 -m 1 > t.aug1f.vg t/17_vg_augment.t: line 150: 1197053 Illegal instruction (core dumped) vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197054 Illegal instruction | vg augment t.vg - -N 0.1 > t.aug1nf.vg t/17_vg_augment.t: line 157: 1197061 Illegal instruction (core dumped) vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx 1197062 (core dumped) | vg augment t.vg - -N 1 -m 0 > t.augr1.vg t/17_vg_augment.t: line 162: 1197068 Illegal instruction (core dumped) vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx 1197069 (core dumped) | vg augment t.vg - -N 0.5 -m 1 > t.augr1f.vg t/17_vg_augment.t: line 167: 1197075 Illegal instruction (core dumped) vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx 1197076 (core dumped) | vg augment t.vg - -N 0.1 > t.augr1nf.vg t/17_vg_augment.t: line 174: 1197083 Illegal instruction (core dumped) vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197084 (core dumped) | vg augment t.vg - -N 1 -m 0 > t.aug1.vg t/17_vg_augment.t: line 177: 1197091 Illegal instruction (core dumped) vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197092 Illegal instruction | vg augment t.vg - -N 0.5 -m 1 > t.aug1.vg t/17_vg_augment.t: line 180: 1197099 Illegal instruction (core dumped) vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx 1197100 Illegal instruction | vg augment t.vg - -N 0.1 > t.aug1.vg t/17_vg_augment.t: line 185: 1197108 Illegal instruction (core dumped) vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx 1197109 (core dumped) | vg augment t.vg - -N 1 -m 0 > t.aug1.vg t/17_vg_augment.t: line 188: 1197116 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx 1197117 Illegal instruction (core dumped) | vg augment t.vg - -N 0.5 -m 1 > t.aug1.vg t/17_vg_augment.t: line 191: 1197124 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx 1197125 Illegal instruction (core dumped) | vg augment t.vg - -N 0.1 > t.aug1.vg t/17_vg_augment.t: line 196: 1197133 Illegal instruction (core dumped) vg map -s CAAATANNNAGGCTTGGAAATTTTCTGGAGTTCTATTATATNNNNNTCCAACTCTCTG -d t.idx > t.gam t/17_vg_augment.t: line 197: 1197134 Illegal instruction (core dumped) vg augment t.vg t.gam -N 0.5 -A t.aug1.gam > t.aug1.vg t/17_vg_augment.t: line 202: 1197141 Illegal instruction (core dumped) vg map -s CAGAGAGTTGGANNNNNATATAATAGAACTCCAGAAAATTTCCAAGCCTNNNTATTTG -d t.idx > t.gam t/17_vg_augment.t: line 203: 1197142 Illegal instruction (core dumped) vg augment t.vg t.gam -N 0.5 -A t.aug1.gam > t.aug1.vg t/17_vg_augment.t ..... 1..39 not ok 1 - direct augmentation embeds reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 # got: '' # expected: '18' not ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes # got: '' # expected: '18' not ok 6 - direct augmentation embeds reads fully for probable errors # got: '0' # expected: '3' not ok 7 - adding a probable error by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 8 - path inclusion does not modify the graph when alignment is a perfect match # got: '0' # expected: '1' not ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold # got: '0' # expected: '1' not ok 10 - unnamed test # got: '50M' # expected: 'path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold' not ok 11 - output GAM has single edit when SNP was filtered out due to coverage # got: '0' # expected: '1' not ok 12 - path inclusion with a complex variant introduces the right number of nodes # got: '0' # expected: '5' not ok 13 - path inclusion works for deletions # got: '0' # expected: '1' not ok 14 - SNPs can be included in the graph # got: '0' # expected: '4' not ok 15 - unnamed test # got: 'GGGGG' # expected: 'a soft clip at read start becomes a new head of the graph' not ok 16 - unnamed test # got: 'AAAAAAAA' # expected: 'a soft clip at read end becomes a new tail of the graph' not ok 17 - augment -s works as desired # got: '0' # expected: '1' not ok 18 - the expected graph translation is exported when the graph is edited # got: '0' # expected: '1290' not ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes # got: '0' # expected: '7' ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps not ok 22 - augmenting with 2snps makes correct number of nodes # got: '0' # expected: '7' not ok 23 - low-quality snp is filtered # got: '0' # expected: '4' ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph 0a1 > GGNGG not ok 26 - augmenting between nodes without filters works as expected # got: '1' # expected: '0' 0a1 > GGNGG not ok 27 - augmenting between nodes with inactive filters works as expected # got: '1' # expected: '0' ok 28 - augmenting between nodes N filter works as expected 0a1 > GGNGG not ok 29 - augmenting between nodes without filters works as expected on reverse strand # got: '1' # expected: '0' 0a1 > GGNGG not ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand # got: '1' # expected: '0' ok 31 - augmenting between nodes N filter works as expected on reverse strand not ok 32 - augmenting within node without filters works as expected # got: '0' # expected: '1' not ok 33 - augmenting within node with inactive filters works as expected # got: '0' # expected: '1' ok 34 - augmenting within node with N filter works as expected not ok 35 - augmenting within node without filters works as expected on reverse strand # got: '0' # expected: '1' not ok 36 - augmenting within node with inactive filters works as expected on reverse strand # got: '0' # expected: '1' ok 37 - augmenting within node with N filter works as expected on reverse strand not ok 38 - unnamed test # got: 'CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG' # expected: 'sequence in filtered alignment has removed insertion' not ok 39 - unnamed test # got: 'CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG' # expected: 'sequence in filtered alignment has removed insertion on reverse strand' Failed 31/39 subtests t/18_vg_call.t: line 13: 1197150 Illegal instruction (core dumped) vg view -J -v call/tiny.json > tiny.vg t/18_vg_call.t: line 17: 1197151 Illegal instruction (core dumped) vg augment tiny.vg empty.gam -A empty_aug.gam > tiny_aug.vg t/18_vg_call.t: line 18: 1197152 Illegal instruction (core dumped) vg index tiny_aug.vg -x tiny_aug.xg t/18_vg_call.t: line 19: 1197153 Illegal instruction (core dumped) vg pack -x tiny_aug.xg -g empty_aug.gam -o tiny_aug.pack t/18_vg_call.t: line 20: 1197154 Illegal instruction (core dumped) vg call tiny_aug.xg -k tiny_aug.pack > tiny_aug.vcf t/18_vg_call.t: line 26: 1197159 Illegal instruction (core dumped) vg construct -r inverting/miniFasta.fa -v inverting/miniFasta_VCFinversion.vcf.gz -S > miniFastaGraph.vg t/18_vg_call.t: line 27: 1197160 Illegal instruction (core dumped) vg index -x miniFastaGraph.xg -g miniFastaGraph.gcsa miniFastaGraph.vg t/18_vg_call.t: line 28: 1197161 Illegal instruction (core dumped) vg sim -x miniFastaGraph.xg -n 1000 -l 30 -a -s 1 > miniFasta.gam t/18_vg_call.t: line 29: 1197162 Illegal instruction (core dumped) vg map -G miniFasta.gam -g miniFastaGraph.gcsa -x miniFastaGraph.xg > miniFastaGraph.gam t/18_vg_call.t: line 30: 1197163 Illegal instruction (core dumped) vg augment miniFastaGraph.vg miniFastaGraph.gam -A mappedminitest_aug.gam > mappedminitest_aug.vg t/18_vg_call.t: line 31: 1197164 Illegal instruction (core dumped) vg index mappedminitest_aug.vg -x mappedminitest_aug.xg t/18_vg_call.t: line 32: 1197165 Illegal instruction (core dumped) vg pack -x mappedminitest_aug.xg -g mappedminitest_aug.gam -o mappedminitest_aug.pack t/18_vg_call.t: line 33: 1197166 Illegal instruction (core dumped) vg call mappedminitest_aug.xg -k mappedminitest_aug.pack > calledminitest.vcf t/18_vg_call.t: line 40: 1197172 Illegal instruction (core dumped) vg construct -r inverting/miniFasta.fa -v inverting/miniFasta_VCFinversion.vcf.gz -S > miniFastaGraph.vg t/18_vg_call.t: line 41: 1197173 Illegal instruction (core dumped) vg index -x miniFastaGraph.xg -g miniFastaGraph.gcsa miniFastaGraph.vg t/18_vg_call.t: line 42: 1197174 Illegal instruction (core dumped) vg sim -x miniFastaGraph.xg -n 1000 -l 30 -a -s 1 > miniFasta.gam t/18_vg_call.t: line 43: 1197175 Illegal instruction (core dumped) vg construct -r inverting/miniFasta.fa > miniFastaFlat.vg t/18_vg_call.t: line 44: 1197176 Illegal instruction (core dumped) vg sim -x miniFastaFlat.vg -n 500 -l 30 -a -s 1 >> miniFasta.gam t/18_vg_call.t: line 45: 1197177 Illegal instruction (core dumped) vg map -G miniFasta.gam -g miniFastaGraph.gcsa -x miniFastaGraph.xg > miniFastaGraph.gam t/18_vg_call.t: line 46: 1197178 Illegal instruction (core dumped) vg augment miniFastaGraph.vg miniFastaGraph.gam -A mappedminitest_aug.gam > mappedminitest_aug.vg t/18_vg_call.t: line 47: 1197179 Illegal instruction (core dumped) vg index mappedminitest_aug.vg -x mappedminitest_aug.xg t/18_vg_call.t: line 48: 1197180 Illegal instruction (core dumped) vg pack -x mappedminitest_aug.xg -g mappedminitest_aug.gam -o mappedminitest_aug.pack t/18_vg_call.t: line 49: 1197181 Illegal instruction (core dumped) vg call mappedminitest_aug.xg -k mappedminitest_aug.pack -d 1 > calledminitest.vcf t/18_vg_call.t: line 58: 1197187 Illegal instruction (core dumped) vg augment -i call/HGSVC_chr22_17119590_17880307.vg call/HGSVC_chr22_17119590_17880307_alts.gam > HGSVC_alts.vg t/18_vg_call.t: line 60: 1197188 Illegal instruction (core dumped) vg index HGSVC_alts.vg -x HGSVC_alts.xg -L t/18_vg_call.t: line 62: 1197189 Illegal instruction (core dumped) vg pack -x HGSVC_alts.xg -g call/HGSVC_chr22_17119590_17880307.gam -o HGSVC_alts.pack t/18_vg_call.t: line 64: 1197190 Illegal instruction (core dumped) vg call HGSVC_alts.xg -k HGSVC_alts.pack -v call/HGSVC_chr22_17200000_17800000.vcf.gz -s HG00514 > HGSVC.vcf t/18_vg_call.t: line 74: 1197205 Illegal instruction (core dumped) vg call HGSVC_alts.xg -k HGSVC_alts.pack -v call/HGSVC_chr22_17200000_17800000.vcf.gz -s HG00514 -d 1 > HGSVC1.vcf t/18_vg_call.t: line 84: 1197221 Illegal instruction (core dumped) vg call HGSVC_alts.xg -k HGSVC_alts.pack -s HG00514 -a > HGSVC2.vcf t/18_vg_call.t: line 92: 1197230 Illegal instruction (core dumped) vg index HGSVC_alts.xg -F HGSVC_travs.gaf.gz -G HGSVC_travs.gbwt t/18_vg_call.t: line 93: 1197231 Illegal instruction (core dumped) vg call HGSVC_alts.xg -k HGSVC_alts.pack -g HGSVC_travs.gbwt -s HG00514 > HGSVC_travs.vcf t/18_vg_call.t: line 94: 1197232 Illegal instruction (core dumped) vg call HGSVC_alts.xg -k HGSVC_alts.pack -s HG00514 > HGSVC_direct.vcf t/18_vg_call.t: line 111: 1197256 Illegal instruction (core dumped) vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg t/18_vg_call.t: line 112: 1197257 Illegal instruction (core dumped) vg index -x x.xg x.vg -L t/18_vg_call.t: line 113: 1197258 Illegal instruction (core dumped) vg sim -s 1 -n 1000 -l 150 -x x.xg -a > sim.gam t/18_vg_call.t: line 114: 1197259 Illegal instruction (core dumped) vg pack -x x.xg -g sim.gam -o x.xg.cx t/18_vg_call.t: line 115: 1197260 Illegal instruction (core dumped) vg pack -x x.vg -g sim.gam -o x.vg.cx t/18_vg_call.t: line 116: 1197261 Illegal instruction (core dumped) vg snarls x.xg > x.snarls t/18_vg_call.t: line 117: 1197262 Illegal instruction (core dumped) vg call x.xg -k x.xg.cx -r x.snarls -t 1 > x.xg.vcf t/18_vg_call.t: line 118: 1197263 Illegal instruction (core dumped) vg call x.vg -k x.vg.cx -r x.snarls -t 1 > x.vg.vcf t/18_vg_call.t: line 122: 1197265 Illegal instruction (core dumped) vg call x.xg -k x.xg.cx -r x.snarls -t 1 -v tiny/tiny.vcf.gz > x.xg.gt.vcf t/18_vg_call.t: line 123: 1197266 Illegal instruction (core dumped) vg call x.vg -k x.vg.cx -r x.snarls -t 1 -v tiny/tiny.vcf.gz > x.vg.gt.vcf t/18_vg_call.t: line 130: 1197269 Illegal instruction (core dumped) vg msga -f msgas/cycle.fa -b s1 -w 64 -t 1 > c.vg t/18_vg_call.t: line 131: 1197270 Illegal instruction (core dumped) vg index -x c.xg -g c.gcsa c.vg t/18_vg_call.t: line 137: 1197273 Illegal instruction (core dumped) vg construct -r m.fa > m.vg t/18_vg_call.t: line 138: 1197274 Illegal instruction (core dumped) vg index -x m.xg m.vg t/18_vg_call.t: line 139: 1197275 Illegal instruction (core dumped) vg sim -n 200 -s 23823 -l 50 -x m.xg -a > m.sim t/18_vg_call.t: line 140: 1197276 Illegal instruction (core dumped) vg map -x c.xg -g c.gcsa -G m.sim > m.gam t/18_vg_call.t: line 141: 1197277 Illegal instruction (core dumped) vg augment c.vg m.gam -A m.aug.gam > c.aug.vg t/18_vg_call.t: line 142: 1197278 Illegal instruction (core dumped) vg index -x c.aug.xg c.aug.vg t/18_vg_call.t: line 143: 1197279 Illegal instruction (core dumped) vg pack -x c.aug.xg -g m.aug.gam -o m.aug.pack t/18_vg_call.t: line 144: 1197280 Illegal instruction (core dumped) vg call c.aug.xg -k m.aug.pack > m.vcf t/18_vg_call.t: line 149: 1197287 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg t/18_vg_call.t: line 150: 1197288 Illegal instruction (core dumped) vg index -G x.gbwt -v small/x.vcf.gz x.vg t/18_vg_call.t: line 152: 1197289 Illegal instruction (core dumped) vg paths -g x.gbwt -V -Q _thread_1_x_0_0 0 -x x.vg >> x.vg t/18_vg_call.t: line 153: 1197290 Illegal instruction (core dumped) vg paths -g x.gbwt -V -Q _thread_1_x_1_0 0 -x x.vg >> x.vg t/18_vg_call.t: line 154: 1197291 Illegal instruction (core dumped) vg sim -x x.vg -P _thread_1_x_0_0 -n 500 -a -s 23 > sim.gam t/18_vg_call.t: line 155: 1197292 Illegal instruction (core dumped) vg sim -x x.vg -P _thread_1_x_1_0 -n 500 -a -s 23 >> sim.gam t/18_vg_call.t: line 157: 1197293 Illegal instruction (core dumped) vg pack -x x.vg -o x.pack -g sim.gam t/18_vg_call.t: line 158: 1197294 Illegal instruction (core dumped) vg call x.vg -k x.pack > call.vcf t/18_vg_call.t: line 159: 1197295 Illegal instruction (core dumped) vg call x.vg -k x.pack -g x.gbwt > callg.vcf t/18_vg_call.t ........ 1..12 ok 1 - calling empty gam gives empty VCF not ok 2 - Called microinversion # got: '0' # expected: '1' ok 3 - Called no microinversion with haploid setting not ok 4 - Fewer than 8 differences between called and true SV genotypes # got: '0' # expected: '1' not ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes # got: '0' # expected: '1' ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg not ok 11 - vg call finds true homozygous variants in a cyclic graph # got: '0' # expected: '3' ok 12 - vg call finds same variants when using gbwt to enumerate traversals Failed 4/12 subtests t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 0 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 0 triples t/20_vgtordf.t ........ 1..6 not ok 1 - vg view produces the expected number of lines of turtle # got: '0' # expected: '90' not ok 2 - vg view produces the expected number of lines of turtle # got: '0' # expected: '90' ok 3 - rapper passed ok 4 - rapper passed not ok 5 - vg view produces the expected number of lines of turtle # got: '0' # expected: '5' not ok 6 - vg view produces the expected number of lines of turtle # got: '0' # expected: '5' Failed 4/6 subtests t/21_vg_filter.t: line 10: 1197332 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/21_vg_filter.t: line 11: 1197333 Illegal instruction (core dumped) vg index -x x.xg x.vg t/21_vg_filter.t: line 12: 1197334 Illegal instruction (core dumped) vg sim -x x.xg -l 100 -n 5000 -e 0.01 -i 0.001 -a > x.gam t/21_vg_filter.t: line 49: 1197352 Illegal instruction (core dumped) vg surject -x x.xg -s -i paired.gam > paired.sam [main_samview] fail to read the header from "paired.sam". t/21_vg_filter.t: line 49: 1197361 Illegal instruction (core dumped) vg surject -x x.xg -s single.gam > single.sam [main_samview] fail to read the header from "single.sam". t/21_vg_filter.t: line 51: 1197370 Illegal instruction (core dumped) vg filter -d 123.5 -t 10 paired.gam > filtered.gam t/21_vg_filter.t: line 56: 1197378 Illegal instruction (core dumped) vg filter -d 0.2 -t 10 single.gam > filtered.gam t/21_vg_filter.t: line 60: 1197385 Illegal instruction (core dumped) vg annotate -p -x x.xg -a paired.gam > paired.annotated.gam t/21_vg_filter.t ...... 1..10 not ok 1 - vg filter with no options preserves input. # got: '0' # expected: '5000' not ok 2 - vg filter downsamples correctly # got: '1' # expected: '0' ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads not ok 5 - reads with refpos annotations not matching an exclusion regex are let through # got: '0' # expected: '200' ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - read pairs can be tropped by feature not ok 10 - read pairs can be kept if only one read fails # got: '0' # expected: '2' Failed 4/10 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t: line 10: 1197427 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz 1197428 Illegal instruction | vg circularize -p x - > circular.vg t/25_circularize.t: line 14: 1197433 Illegal instruction (core dumped) vg index -x circular.xg circular.vg t/25_circularize.t: line 15: 1197434 Illegal instruction (core dumped) vg convert circular.xg -v > extracted.vg t/25_circularize.t .... 1..2 not ok 1 - a path may be circularized # got: '0' # expected: '1' not ok 2 - a circular path survives a round trip to/from xg # got: '0' # expected: '1' Failed 2/2 subtests t/26_deconstruct.t: line 10: 1197441 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg t/26_deconstruct.t: line 11: 1197442 Illegal instruction (core dumped) vg index tiny.vg -x tiny.xg t/26_deconstruct.t: line 12: 1197443 Illegal instruction (core dumped) vg deconstruct tiny.xg -p x -t 1 > tiny_decon.vcf t/26_deconstruct.t: line 21: 1197453 Illegal instruction (core dumped) vg msga -f GRCh38_alts/FASTA/HLA/V-352962.fa -t 1 -k 16 1197454 (core dumped) | vg mod -U 10 - 1197455 (core dumped) | vg mod -c - > hla.vg t/26_deconstruct.t: line 22: 1197456 Illegal instruction (core dumped) vg index hla.vg -x hla.xg t/26_deconstruct.t: line 24: 1197457 Illegal instruction (core dumped) vg deconstruct hla.xg -p "gi|157734152:29563108-29564082" > hla_decon.vcf t/26_deconstruct.t: line 27: 1197465 Illegal instruction (core dumped) vg deconstruct hla.xg -p "gi|568815592:29791752-29792749" > hla_decon.vcf t/26_deconstruct.t: line 31: 1197473 Illegal instruction (core dumped) vg deconstruct hla.xg -p "gi|568815592:29791752-29792749" -e > hla_decon_path.vcf t/26_deconstruct.t: line 51: 1197506 Illegal instruction (core dumped) vg view -Fv inv.gfa > inv.vg t/26_deconstruct.t: line 52: 1197507 Illegal instruction (core dumped) vg index inv.vg -x inv.xg t/26_deconstruct.t: line 53: 1197508 Illegal instruction (core dumped) vg deconstruct inv.xg -p x -e > inv_decon.vcf t/26_deconstruct.t: line 61: 1197513 Illegal instruction (core dumped) vg deconstruct inv.xg -p y -e > inv_decon.vcf t/26_deconstruct.t: line 70: 1197518 Illegal instruction (core dumped) vg construct -v small/x.vcf.gz -r small/x.fa 1197519 (core dumped) | vg view -g - > cyclic_small.gfa t/26_deconstruct.t: line 73: 1197520 Illegal instruction (core dumped) vg view -Fv cyclic_small.gfa > cyclic_small.vg t/26_deconstruct.t: line 74: 1197521 Illegal instruction (core dumped) vg index cyclic_small.vg -x cyclic_small.xg t/26_deconstruct.t: line 75: 1197522 Illegal instruction (core dumped) vg deconstruct cyclic_small.xg -p y -e > cyclic_small_decon.vcf t/26_deconstruct.t: line 83: 1197527 Illegal instruction (core dumped) vg deconstruct cyclic_small.xg -p x -e > cyclic_small_decon.vcf t/26_deconstruct.t: line 91: 1197532 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa 1197533 (core dumped) | vg view -g - > cyclic_tiny.gfa t/26_deconstruct.t: line 94: 1197534 Illegal instruction (core dumped) vg view -Fv cyclic_tiny.gfa > cyclic_tiny.vg t/26_deconstruct.t: line 95: 1197535 Illegal instruction (core dumped) vg index cyclic_tiny.vg -x cyclic_tiny.xg t/26_deconstruct.t: line 96: 1197536 Illegal instruction (core dumped) vg find -x cyclic_tiny.xg -n 10 -n 11 -n 12 -n 13 -n 14 -n 15 -c 1 > cycle.vg t/26_deconstruct.t: line 97: 1197537 Illegal instruction (core dumped) vg index cycle.vg -x cycle.xg t/26_deconstruct.t: line 98: 1197538 Illegal instruction (core dumped) vg deconstruct cycle.xg -p y -e -t 1 > cycle_decon.vcf t/26_deconstruct.t: line 110: 1197551 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa 1197552 (core dumped) | vg view -g - > tiny_names.gfa t/26_deconstruct.t: line 116: 1197553 Illegal instruction (core dumped) vg view -Fv tiny_names.gfa > tiny_names.vg t/26_deconstruct.t: line 117: 1197554 Illegal instruction (core dumped) vg index tiny_names.vg -x tiny_names.xg t/26_deconstruct.t .... 1..19 1,3d0 < x 14 G A < x 34 T A < x 39 T A not ok 1 - deconstruct retrieved original VCF (modulo adjacent snp allele) # got: '1' # expected: '0' not ok 2 - deconstructed hla vcf has correct number of sites # got: '0' # expected: '17' not ok 3 - unnamed test # got: 'C-CGCGGGCGCCGTGGATGGAGCA' # expected: 'deconstructed hla vcf has correct insertion' not ok 4 - deconstructed hla vcf with other path has correct number of sites # got: '0' # expected: '17' not ok 5 - unnamed test # got: 'CGCGGGCGCCGTGGATGGAGCA-C' # expected: 'deconstructed hla vcf has correct deletion' ok 6 - path-based and exhaustive decontruction give equivalent sites when expected not ok 7 - unnamed test # got: '1' # expected: 'path that differs from reference in every alt has correct genotype' not ok 8 - unnamed test # got: '0' # expected: 'path that is same as reference in every alt has correct genotype' not ok 9 - unnamed test # got: '##contig=' # expected: 'reference contig correctly written' 0a1 > x 10 CTTGGAAATTTTCTGGAGTT AACTCCAGAAAATTTCCAAG 1 not ok 10 - deconstruct correctly handles a simple inversion # got: '1' # expected: '0' 0a1 > y 10 AACTCCAGAAAATTTCCAAG CTTGGAAATTTTCTGGAGTT 1 not ok 11 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge # got: '1' # expected: '0' 0a1 > y 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA 1 not ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl # got: '1' # expected: '0' 0a1 > x 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA 1 not ok 13 - deconstruct correctly handles a cycle in the alt path # got: '1' # expected: '0' not ok 14 - cyclic reference deconstruction has correct number of variants # got: '0' # expected: '2' 0a1,2 > y 20 T A 0 > y 44 A T 1 not ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl # got: '1' # expected: '0' not ok 16 - -P -A options return correct number of variants # got: '0' # expected: '2' not ok 17 - -P -A options use correct reference name # got: '0' # expected: '2' not ok 18 - -P -A identifies conflict in alt1 in second variant # got: '0' # expected: '1' ok 19 - deconstructing vg graph gives same output as xg graph Failed 17/19 subtests t/27_vg_genotype.t: line 11: 1197575 Illegal instruction (core dumped) vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg t/27_vg_genotype.t: line 12: 1197576 Illegal instruction (core dumped) vg index -x tiny.vg.xg -g tiny.vg.gcsa -k 16 tiny.vg t/27_vg_genotype.t: line 13: 1197577 Illegal instruction (core dumped) vg sim -n 100 -x tiny.vg.xg -l 30 > reads.txt t/27_vg_genotype.t: line 14: 1197578 Illegal instruction (core dumped) vg map -T reads.txt -g tiny.vg.gcsa -x tiny.vg.xg > tiny.gam t/27_vg_genotype.t: line 16: 1197579 Illegal instruction (core dumped) vg genotype tiny.vg tiny.gam > /dev/null t/27_vg_genotype.t: line 19: 1197580 Illegal instruction (core dumped) vg genotype tiny.vg tiny.gam -v > /dev/null t/27_vg_genotype.t: line 24: 1197582 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa > flat.vg t/27_vg_genotype.t: line 25: 1197583 Illegal instruction (core dumped) vg index -x flat.xg -g flat.gcsa -k 8 flat.vg t/27_vg_genotype.t: line 28: 1197586 Illegal instruction (core dumped) vg construct -r flat1.fa > flat1.vg t/27_vg_genotype.t: line 29: 1197587 Illegal instruction (core dumped) vg index -x flat1.xg flat1.vg t/27_vg_genotype.t: line 33: 1197591 Illegal instruction (core dumped) vg construct -r flat2.fa > flat2.vg t/27_vg_genotype.t: line 34: 1197592 Illegal instruction (core dumped) vg index -x flat2.xg flat2.vg t/27_vg_genotype.t: line 36: 1197595 Illegal instruction (core dumped) vg map -x flat.xg -g flat.gcsa -G <(cat flat1.sim flat2.sim) > flat.gam t/27_vg_genotype.t: line 37: 1197597 Illegal instruction (core dumped) vg genotype flat.vg flat.gam -t 1 > flat.loci t/27_vg_genotype.t: line 39: 1197599 Illegal instruction (core dumped) vg msga -f flats.fa -b x 1197600 (core dumped) | vg paths -d -v - 1197601 (core dumped) | vg mod -n - 1197602 (core dumped) | vg mod -c - > flat_msga.vg t/27_vg_genotype.t: line 40: 1197603 Illegal instruction (core dumped) vg augment flat.vg -L flat.loci 1197604 (core dumped) | vg paths -d -v - 1197605 Illegal instruction | vg mod -n - 1197606 (core dumped) | vg mod -c - > flat_mod.vg t/27_vg_genotype.t: line 46: 1197621 Illegal instruction (core dumped) vg view -q flat.loci 1197622 (core dumped) | vg view -qJz - 1197623 (core dumped) | vg view -q - > /dev/null t/27_vg_genotype.t: line 51: 1197625 Illegal instruction (core dumped) vg construct -v call/bigins.vcf.gz -r tiny/tiny.fa > bigins.vg t/27_vg_genotype.t: line 52: 1197626 Illegal instruction (core dumped) vg index -x bigins.vg.xg -g bigins.vg.gcsa -k 16 bigins.vg t/27_vg_genotype.t: line 54: 1197628 Illegal instruction (core dumped) vg map -T reads.txt -g bigins.vg.gcsa -x bigins.vg.xg > bigins.gam t/27_vg_genotype.t .... 1..5 not ok 1 - vg genotype runs successfully # got: '132' # expected: '0' not ok 2 - vg genotype runs successfully when emitting vcf # got: '132' # expected: '0' ok 3 - called genotypes are correct in a small simulated example not ok 4 - genotype format can be converted to and from JSON # got: '132' # expected: '0' not ok 5 - genotype finds big insert # got: '0' # expected: '1' Failed 4/5 subtests t/28_translate.t: line 10: 1197635 Illegal instruction (core dumped) vg construct -m 1000 -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg t/28_translate.t: line 11: 1197636 Illegal instruction (core dumped) vg index -x tiny.xg -g tiny.gcsa -k 16 tiny.vg t/28_translate.t: line 12: 1197637 Illegal instruction (core dumped) vg sim -n 5 -e 0.01 -i 0.005 -x tiny.xg -l 30 -a 1197638 (core dumped) | vg view -a - 1197639 Done | sort 1197640 (core dumped) | vg view -JGa - > tiny.sim t/28_translate.t: line 13: 1197641 Illegal instruction (core dumped) vg map -G tiny.sim -x tiny.xg -g tiny.gcsa -t 1 > tiny.gam t/28_translate.t: line 14: 1197642 Illegal instruction (core dumped) vg augment -Z tiny.trans -i tiny.vg tiny.gam > tiny.mod.vg t/28_translate.t: line 15: 1197643 Illegal instruction (core dumped) vg paths -v tiny.mod.vg -X 1197644 (core dumped) | vg view -a - 1197645 Exit 1 | grep -v x 1197646 Done | sort 1197647 (core dumped) | vg view -JGa - > tiny.paths.gam t/28_translate.t: line 16: 1197648 Illegal instruction vg translate -a tiny.paths.gam tiny.trans 1197649 Illegal instruction (core dumped) | vg view -a - 1197650 Done | sort 1197651 Illegal instruction (core dumped) | vg view -JGa - > tiny.paths.trans.gam t/28_translate.t: line 17: 1197652 Illegal instruction (core dumped) vg augment -Z tiny.trans.1 -i tiny.vg tiny.paths.trans.gam > tiny.mod.vg.1 t/28_translate.t: line 23: 1197672 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa > flat.vg t/28_translate.t: line 24: 1197673 Illegal instruction (core dumped) vg index -x flat.xg -g flat.gcsa -k 8 flat.vg t/28_translate.t: line 25: 1197674 Illegal instruction (core dumped) vg map -x flat.xg -g flat.gcsa -G tiny/flat-s69-n1-l50-e0.05.gam > flat.gam t/28_translate.t: line 26: 1197675 Illegal instruction (core dumped) vg augment -i -Z flat1.trans flat.vg flat.gam > flat1.vg t/28_translate.t: line 27: 1197676 Illegal instruction (core dumped) vg index -x flat1.xg -g flat1.gcsa -k 8 flat1.vg t/28_translate.t: line 28: 1197677 Illegal instruction (core dumped) vg map -x flat1.xg -g flat1.gcsa -G tiny/flat1-s77-n1-l50-e0.05.gam > flat1.gam t/28_translate.t: line 29: 1197678 Illegal instruction (core dumped) vg augment -i -Z flat2.trans flat1.vg flat1.gam > flat2.vg t/28_translate.t: line 30: 1197679 Illegal instruction (core dumped) vg translate -o flat2.trans flat1.trans > flatover.trans t/28_translate.t: line 31: 1197680 Illegal instruction (core dumped) vg paths -v flat2.vg -X 1197681 (core dumped) | vg view -a - 1197682 Exit 1 | grep -v x 1197683 (core dumped) | vg view -JGa - > flat2.paths.gam t/28_translate.t: line 32: 1197684 Illegal instruction (core dumped) vg translate -a flat2.paths.gam flatover.trans > flatback.gam t/28_translate.t: line 33: 1197685 Illegal instruction (core dumped) vg augment -i flat.vg flatback.gam > flat2back.vg t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests t/30_vg_chunk.t: line 11: 1197695 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz -a > x.vg t/30_vg_chunk.t: line 12: 1197696 Illegal instruction (core dumped) vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg t/30_vg_chunk.t: line 13: 1197697 Illegal instruction (core dumped) vg view -a small/x-l100-n1000-s10-e0.01-i0.01.gam > x.gam.json t/30_vg_chunk.t: line 27: 1197726 Illegal instruction (core dumped) vg chunk -x x.xg -p x -s 233 -o 50 -b _chunk_test -c 0 -t 2 t/30_vg_chunk.t: line 28: 1197727 Illegal instruction (core dumped) vg chunk -x x.xg -p x -s 233 -o 50 -b _chunk_test -c 0 -t 1 ls: cannot access '_chunk_test*.vg': No such file or directory t/30_vg_chunk.t: line 33: 1197732 Illegal instruction (core dumped) vg gamsort small/x-l100-n1000-s10-e0.01-i0.01.gam -i x.sorted.gam.gai > x.sorted.gam t/30_vg_chunk.t: line 35: 1197733 Illegal instruction (core dumped) vg chunk -x x.xg -a x.sorted.gam -g -b _chunk_test -e _chunk_test_bed.bed -E _chunk_test_out.bed -c 0 ls: cannot access '_chunk_test*.vg': No such file or directory ls: cannot access '_chunk_test*.gam': No such file or directory grep: _chunk_test_out.bed: No such file or directory t/30_vg_chunk.t: line 54: 1197786 Illegal instruction (core dumped) vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg t/30_vg_chunk.t: line 56: 1197788 Illegal instruction (core dumped) vg chunk -x x.xg -n 5 -b x.chunk/ cat: 'x.chunk/*vg': No such file or directory t/30_vg_chunk.t: line 65: 1197805 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz > xy.vg t/30_vg_chunk.t: line 66: 1197806 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz -R x > x.vg t/30_vg_chunk.t: line 67: 1197807 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz -R y > y.vg t/30_vg_chunk.t: line 68: 1197808 Illegal instruction (core dumped) vg ids -j x.vg y.vg t/30_vg_chunk.t: line 69: 1197809 Illegal instruction (core dumped) vg sim -x x.vg -n 50 -a > x.gam t/30_vg_chunk.t: line 70: 1197810 Illegal instruction (core dumped) vg sim -x y.vg -n 100 -a > y.gam t/30_vg_chunk.t: line 73: 1197812 Illegal instruction (core dumped) vg chunk -x xy.vg -M -b path_chunk -O hg -a xy.gam -g t/30_vg_chunk.t: line 82: 1197845 Illegal instruction (core dumped) vg chunk -x xy.vg -C -p x -b path_chunk_ind -O hg -a xy.gam -g > /dev/null t/30_vg_chunk.t: line 83: 1197846 Illegal instruction (core dumped) vg chunk -x xy.vg -C -p y -b path_chunk_ind -O hg -a xy.gam -g > /dev/null t/30_vg_chunk.t: line 86: 1197859 Illegal instruction (core dumped) vg paths -v x.vg -E > x_paths.txt t/30_vg_chunk.t: line 87: 1197860 Illegal instruction (core dumped) vg paths -v path_chunk_x.hg -E > pc_x_paths.txt t/30_vg_chunk.t: line 90: 1197862 Illegal instruction (core dumped) vg chunk -x xy.vg -C -b components_chunk t/30_vg_chunk.t ....... 1..24 not ok 1 - unnamed test # got: '210' # expected: 'vg chunk with no options preserves nodes' not ok 2 - unnamed test # got: '291' # expected: 'vg chunk with no options preserves edges' not ok 3 - chunk has path going through node 9 # got: '0' # expected: '1' not ok 4 - chunk has path going through node 9 # got: '0' # expected: '1' not ok 5 - -s produces correct number of chunks # got: '0' # expected: '6' not ok 6 - gam chunker produces correct number of graphs # got: '0' # expected: '2' not ok 7 - gam chunker produces correct number of gams # got: '0' # expected: '2' not ok 8 - gam chunker produces bed with correct number of chunks # got: '0' # expected: '2' ok 9 - gam chunker emits each matching read at most once not ok 10 - chunk contains the expected number of alignments # got: '0' # expected: '225' not ok 11 - id chunker produces correct chunk size # got: '0' # expected: '3' not ok 12 - id chunker produces correct single chunk # got: '0' # expected: '1' not ok 13 - id chunker traces correct chunk size # got: '0' # expected: '5' ok 14 - chunker extracts no threads from an empty gPBWT not ok 15 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it # got: '0' # expected: '2' not ok 16 - chunker can extract a partial haplotype from a GBWT # got: '' # expected: '3' ok 17 - n-chunking works and chunks over the full graph ok 18 - path-based components finds subgraphs ok 19 - x gam chunk has correct number of reads ok 20 - y gam chunk has correct number of reads ok 21 - x gam chunk has correct number of reads with -p path ok 22 - y gam chunk has correct number of reads with -p path ok 23 - path-based component contains correct path length ok 24 - components finds subgraphs Failed 14/24 subtests t/31_vg_add.t: line 10: 1197876 Illegal instruction (core dumped) vg construct -r add/ref.fa > ref.vg t/31_vg_add.t: line 11: 1197877 Illegal instruction (core dumped) vg add -v add/benedict.vcf ref.vg > benedict.vg t/31_vg_add.t: line 14: 1197878 Illegal instruction (core dumped) vg add -v add/rename.vcf -n chrR=ref ref.vg > benedict2.vg t/31_vg_add.t: line 20: 1197880 Illegal instruction (core dumped) vg convert -p ref.vg > ref.pg t/31_vg_add.t: line 21: 1197881 Illegal instruction (core dumped) vg add -v add/benedict.vcf ref.pg > benedict3.vg t/31_vg_add.t: line 27: 1197883 Illegal instruction (core dumped) vg add -v add/separated.vcf ref.vg > no-n.vg t/31_vg_add.t: line 28: 1197884 Illegal instruction (core dumped) vg construct -r add/refN.fa > refN.vg t/31_vg_add.t: line 29: 1197885 Illegal instruction (core dumped) vg add -v add/separated.vcf refN.vg > with-n.vg t/31_vg_add.t: line 33: 1197894 Illegal instruction (core dumped) vg construct -r add/ngap.fa > ngap.vg t/31_vg_add.t: line 34: 1197895 Illegal instruction (core dumped) vg add -v add/ngap-offset.vcf ngap.vg > ngap-add.vg t/31_vg_add.t: line 39: 1197908 Illegal instruction (core dumped) vg construct -r small/x.fa > x-ref.vg t/31_vg_add.t: line 40: 1197909 Illegal instruction (core dumped) vg add -v small/x.vcf.gz x-ref.vg > x.vg t/31_vg_add.t ......... 1..12 not ok 1 - vg add can create a graph # got: '132' # expected: '0' not ok 2 - vg add can create a graph with contig renames # got: '132' # expected: '0' ok 3 - vg add produces the same graph from VCFs with different contig names not ok 4 - vg add can create a graph from a PackedGraph # got: '132' # expected: '0' ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology not ok 7 - adding variants adds only the alt bases near large N gaps # got: '' # expected: '73315' not ok 8 - vg add can create a slightly larger graph # got: '132' # expected: '0' ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 8/12 subtests t/32_vg_snarls.t: line 10: 1197931 Illegal instruction (core dumped) vg view -J -v snarls/snarls.json > snarls.vg t/32_vg_snarls.t: line 16: 1197940 Illegal instruction (core dumped) vg index snarls.vg -x snarls.xg t/32_vg_snarls.t: line 23: 1197949 Illegal instruction (core dumped) vg construct -Saf -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg t/32_vg_snarls.t: line 24: 1197950 Illegal instruction (core dumped) vg snarls tiny.vg -r tiny.exhaustive.trav > /dev/null t/32_vg_snarls.t: line 25: 1197951 Illegal instruction (core dumped) vg snarls tiny.vg -r tiny.vcf.trav -v tiny/tiny.vcf.gz > /dev/null t/32_vg_snarls.t: line 34: 1197958 Illegal instruction (core dumped) vg construct -Saf -v sv/x.inv.vcf -r sv/x.fa > x.inv.vg t/32_vg_snarls.t: line 35: 1197959 Illegal instruction (core dumped) vg snarls x.inv.vg -a -r x.inv.exhaustive.trav > /dev/null t/32_vg_snarls.t: line 36: 1197960 Illegal instruction (core dumped) vg snarls x.inv.vg -a -r x.inv.vcf.trav -v sv/x.inv.vcf -f sv/x.fa > /dev/null t/32_vg_snarls.t: line 45: 1197967 Illegal instruction (core dumped) vg construct -Saf -v ins_and_del/ins_and_del.vcf.gz -r ins_and_del/ins_and_del.fa > ins_and_del.vg t/32_vg_snarls.t: line 46: 1197968 Illegal instruction (core dumped) vg snarls ins_and_del.vg -r ins_and_del.exhaustive.trav > /dev/null t/32_vg_snarls.t: line 47: 1197969 Illegal instruction (core dumped) vg snarls ins_and_del.vg -r ins_and_del.vcf.trav -v ins_and_del/ins_and_del.vcf.gz > /dev/null t/32_vg_snarls.t: line 56: 1197976 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz > xy.vg t/32_vg_snarls.t: line 57: 1197977 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz -R x > x.vg t/32_vg_snarls.t: line 58: 1197978 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy.vcf.gz -R y > y.vg t/32_vg_snarls.t: line 59: 1197979 Illegal instruction (core dumped) vg snarls x.vg > xy.snarls t/32_vg_snarls.t: line 60: 1197980 Illegal instruction (core dumped) vg snarls y.vg >> xy.snarls t/32_vg_snarls.t ...... 1..9 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 4 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 5 - vcf traversals are the same as exhaustive traversals for tiny graph ok 6 - vcf traversals are the same as exhaustive traversals for inversion ok 7 - vcf traversals are the same as exhaustive traversals for ins_and_del graph not ok 8 - correct number of snarls when parallelizing on compoents # got: '0' # expected: '35' ok 9 - same number of snarls when parallelizing on components Failed 5/9 subtests t/33_vg_mpmap.t: line 13: 1197994 Illegal instruction (core dumped) vg construct -m 1000 -a -r small/xy.fa -v small/xy2.vcf.gz > xy2.vg t/33_vg_mpmap.t: line 14: 1197995 Illegal instruction (core dumped) vg index -x xy2.xg -g xy2.gcsa -v small/xy2.vcf.gz --gbwt-name xy2.gbwt -k 16 xy2.vg t/33_vg_mpmap.t: line 25: 1198009 Illegal instruction (core dumped) vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM > gbwt.gam t/33_vg_mpmap.t: line 36: 1198019 Illegal instruction (core dumped) vg snarls xy2.vg > xy2.snarls t/33_vg_mpmap.t: line 47: 1198037 Illegal instruction (core dumped) vg index -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -k 16 graphs/refonly-lrc_kir.vg t/33_vg_mpmap.t: line 49: 1198038 Illegal instruction (core dumped) vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 10 -D 50 -F GAM 1198039 (core dumped) | vg view -aj - > temp_paired_alignment.json t/33_vg_mpmap.t: line 50: 1198040 Illegal instruction (core dumped) vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 100000 -D 5 -F GAM 1198041 (core dumped) | vg view -aj - > temp_distant_alignment.json t/33_vg_mpmap.t: line 51: 1198042 Illegal instruction (core dumped) vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -F GAM 1198043 Illegal instruction | vg view -aj - > temp_independent_alignment.json t/33_vg_mpmap.t: line 64: 1198075 Illegal instruction (core dumped) vg sim -x graphs/refonly-lrc_kir.vg.xg -n 1000 -p 500 -l 100 -a > input.gam t/33_vg_mpmap.t: line 66: 1198076 Illegal instruction (core dumped) vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -i -F GAM --no-qual-adjust > output.gam t/33_vg_mpmap.t: line 73: 1198082 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg t/33_vg_mpmap.t: line 74: 1198083 Illegal instruction (core dumped) vg index -x t.xg -g t.gcsa -k 16 t.vg rm: cannot remove 't.xg': No such file or directory rm: cannot remove 't.gcsa': No such file or directory rm: cannot remove 't.gcsa.lcp': No such file or directory t/33_vg_mpmap.t: line 95: 1198089 Illegal instruction (core dumped) vg construct -m 32 -r small/x.fa -v small/x.vcf.gz > s.vg t/33_vg_mpmap.t: line 96: 1198090 Illegal instruction (core dumped) vg snarls -T s.vg > s.snarls t/33_vg_mpmap.t: line 97: 1198091 Illegal instruction (core dumped) vg index s.vg -x s.xg -g s.gcsa t/33_vg_mpmap.t: line 98: 1198092 Illegal instruction (core dumped) vg index s.vg -j s.dist -s s.snarls rm: cannot remove 's.xg': No such file or directory rm: cannot remove 's.gcsa': No such file or directory rm: cannot remove 's.gcsa.lcp': No such file or directory rm: cannot remove 's.dist': No such file or directory t/33_vg_mpmap.t ....... 1..17 not ok 1 - MAPQ is 50% without haplotype info # got: '' # expected: '3' not ok 2 - haplotype match can disambiguate # got: '' # expected: '4' not ok 3 - MAPQ is 50% when paired without haplotype info # got: '' # expected: '3' not ok 4 - haplotype match can disambiguate paired # got: '' # expected: '4' not ok 5 - use of haplotype-aware mapping is recorded # got: '' # expected: 'true' not ok 6 - Haplotype-oblivious mapping places read on the wrong contig # got: '' # expected: '50' not ok 7 - Haplotype-oblivious mapping places read with MAPQ of 50% # got: '' # expected: '3' not ok 8 - Haplotype-aware mapping places read on the right contig # got: '' # expected: '1' not ok 9 - Haplotype-aware mapping places read with MAPQ > 50% # got: '' # expected: '6' not ok 10 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 11 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 12 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart # got: '0' # expected: '1' ok 13 - small batches are still all paired in the output not ok 14 - multipath mapping works in scenarios that trigger branch point trimming # got: '0' # expected: '3' not ok 15 - spliced alignments can be found when aligning RNA # got: '' # expected: '108' not ok 16 - paired mapping can identify a splice junction on read 1 # got: '0' # expected: '1' not ok 17 - paired mapping can identify a splice junction on read 2 # got: '0' # expected: '1' Dubious, test returned 1 (wstat 256, 0x100) Failed 16/17 subtests t/34_vg_pack.t: line 10: 1198110 Illegal instruction (core dumped) vg construct -m 1000 -r tiny/tiny.fa > flat.vg t/34_vg_pack.t: line 11: 1198111 Illegal instruction (core dumped) vg view flat.vg 1198112 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' 1198113 (core dumped) | vg view -Fv - > 2snp.vg t/34_vg_pack.t: line 12: 1198114 Illegal instruction (core dumped) vg index -x 2snp.xg 2snp.vg t/34_vg_pack.t: line 13: 1198115 Illegal instruction (core dumped) vg sim -l 30 -x 2snp.xg -n 30 -a > 2snp.sim t/34_vg_pack.t: line 14: 1198116 Illegal instruction (core dumped) vg index -x flat.xg -g flat.gcsa -k 16 flat.vg t/34_vg_pack.t: line 15: 1198117 Illegal instruction (core dumped) vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam t/34_vg_pack.t: line 16: 1198118 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam -e t/34_vg_pack.t: line 20: 1198125 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.snapshot.cx -g pileup/2snp.gam -e t/34_vg_pack.t: line 25: 1198141 Illegal instruction (core dumped) vg pack -x flat.xg -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx -o 2snp.gam.cx.3x (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error t/34_vg_pack.t: line 32: 1198177 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx -b 10 -g 2snp.gam t/34_vg_pack.t: line 44: 1198197 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam t/34_vg_pack.t: line 45: 1198198 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx.3x -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx t/34_vg_pack.t: line 47: 1198202 Done cat 2snp.gam 2snp.gam 2snp.gam 1198203 Illegal instruction (core dumped) | vg pack -x flat.xg -o 2snp.gam.cx -g - t/34_vg_pack.t: line 52: 1198207 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam t/34_vg_pack.t: line 53: 1198208 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx.3x -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx t/34_vg_pack.t: line 55: 1198212 Done cat 2snp.gam 2snp.gam 2snp.gam 1198213 Illegal instruction (core dumped) | vg pack -x flat.xg -o 2snp.gam.cx -g - t/34_vg_pack.t: line 62: 1198218 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg t/34_vg_pack.t: line 63: 1198219 Illegal instruction (core dumped) vg index tiny.vg -x tiny.xg t/34_vg_pack.t: line 73: 1198236 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/34_vg_pack.t: line 74: 1198237 Illegal instruction (core dumped) vg index -x x.xg x.vg t/34_vg_pack.t: line 75: 1198238 Illegal instruction (core dumped) vg sim -s 1 -n 1000 -l 150 -x x.xg -a > sim.gam t/34_vg_pack.t: line 76: 1198239 Illegal instruction (core dumped) vg pack -x x.xg -g sim.gam -o x.xg.cx t/34_vg_pack.t: line 77: 1198240 Illegal instruction (core dumped) vg pack -x x.vg -g sim.gam -o x.vg.cx -t 1 t/34_vg_pack.t: line 96: 1198260 Illegal instruction (core dumped) vg convert x.vg -G sim.gam 1198261 Done | bgzip 1198262 (core dumped) | vg pack -x x.vg -a - -o x.vg.gaf.cx t/34_vg_pack.t: line 107: 1198271 Illegal instruction (core dumped) vg construct -m 5 -r tiny/tiny.fa > flat.vg t/34_vg_pack.t: line 108: 1198272 Illegal instruction (core dumped) vg index flat.vg -g flat.gcsa t/34_vg_pack.t: line 110: 1198273 Illegal instruction (core dumped) vg map -x flat.vg -g flat.gcsa -s CAAATAAGG 1198274 (core dumped) | vg view -a - 1198275 Done | sed -e 's/60/20/g' 1198276 (core dumped) | vg view -JaG - > flat.gam t/34_vg_pack.t: line 112: 1198277 Illegal instruction (core dumped) vg map -x flat.vg -g flat.gcsa -s GGCTTGGAA 1198278 Illegal instruction | vg view -a - 1198279 Done | sed -e 's/60/10/g' 1198280 (core dumped) | vg view -JaG - >> flat.gam t/34_vg_pack.t: line 114: 1198281 Illegal instruction (core dumped) vg map -x flat.vg -g flat.gcsa -s AACTCTCTG 1198282 (core dumped) | vg view -a - 1198283 (core dumped) | vg view -JaG - >> flat.gam t/34_vg_pack.t: line 115: 1198284 Illegal instruction (core dumped) vg pack -x flat.vg -o flat.cx -g flat.gam t/34_vg_pack.t ........ 1..18 not ok 1 - allele observation packing detects 2 SNPs # got: '0' # expected: '2' not ok 2 - pileup packs agree with graph coverage # got: 'f9108e41700ebf9a7be4b41322033704' # expected: 'd41d8cd98f00b204e9800998ecf8427e' not ok 3 - unnamed test # got: 'graph coverages are merged from multiple .cx indexes' # expected: '' not ok 4 - unnamed test # got: 'edit records are merged from multiple .cx indexes' # expected: '' ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges not ok 10 - unnamed test # got: '88' # expected: 'pack computes the same total edge coverage as pileup' not ok 11 - unnamed test # got: 'pack stores the correct edge pileup to disk' # expected: '' ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - unnamed test # got: '20-15-10-10-0-0-0-0-60-60-' # expected: 'average node qualities are correct' Failed 7/18 subtests t/36_vg_annotate.t: line 10: 1198293 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg t/36_vg_annotate.t: line 12: 1198294 Illegal instruction (core dumped) vg mod -N t.vg > t.ref.vg t/36_vg_annotate.t: line 13: 1198295 Illegal instruction (core dumped) vg index -x t.xg t.vg t/36_vg_annotate.t: line 14: 1198296 Illegal instruction (core dumped) vg index -x t.ref.xg t.ref.vg t/36_vg_annotate.t: line 18: 1198301 Illegal instruction (core dumped) vg annotate -b tiny/tiny.bed -x t.ref.xg -a tiny/tiny-s543-n30-l10.gam > annotated.gam t/36_vg_annotate.t: line 27: 1198334 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/36_vg_annotate.t: line 28: 1198335 Illegal instruction (core dumped) vg index -x x.xg x.vg t/36_vg_annotate.t: line 30: 1198336 Illegal instruction (core dumped) vg annotate -p -x x.xg -a small/x-s1337-n1.gam > annot.gam t/36_vg_annotate.t: line 37: 1198348 Illegal instruction (core dumped) vg view -Jv cyclic/circular_path.json > circular_path.vg t/36_vg_annotate.t: line 38: 1198349 Illegal instruction (core dumped) vg index -x circular_path.xg circular_path.vg t/36_vg_annotate.t: line 39: 1198350 Illegal instruction (core dumped) vg annotate -p -x circular_path.xg -b cyclic/circular_path_origin.bed > circular_path_origin.gam t/36_vg_annotate.t .... 1..9 not ok 1 - we can detect when reads contain non-reference variation # got: '0' # expected: '10' not ok 2 - vg annotate finds the right number of reads overlapping a feature # got: '0' # expected: '3' ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features not ok 5 - vg annotate shows reads having to go through one feature to get to another at the end # got: '0' # expected: '2' not ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature # got: '0' # expected: '30' not ok 7 - annotating with earliest path position produces one position # got: '0' # expected: '1' not ok 8 - annotating with multiple path positions produces multiple positions # got: '0' # expected: '13' not ok 9 - annotations derived from BED can span the end/start joins of circular paths # got: '' # expected: '{"node_id":"1","offset":"5"} # {"node_id":"1"}' Failed 7/9 subtests t/37_vg_gbwt.t: line 12: 1198357 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/37_vg_gbwt.t: line 13: 1198358 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null t/37_vg_gbwt.t: line 14: 1198359 Illegal instruction (core dumped) vg ids -j x.vg y.vg t/37_vg_gbwt.t: line 16: 1198360 Illegal instruction (core dumped) vg index -x x.xg x.vg t/37_vg_gbwt.t: line 17: 1198361 Illegal instruction (core dumped) vg index -x xy.xg x.vg y.vg t/37_vg_gbwt.t: line 18: 1198362 Illegal instruction (core dumped) vg index -x xy-alt.xg -L x.vg y.vg t/37_vg_gbwt.t: line 22: 1198363 Illegal instruction (core dumped) vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 24: 1198364 Illegal instruction (core dumped) vg index -G x2.gbwt -v small/xy2.vcf.gz x.vg cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 28: 1198366 Illegal instruction (core dumped) vg gbwt -x x.vg -o parse --parse-only -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 32: 1198368 Illegal instruction (core dumped) vg view -x GBWT x.gbwt > x.bare.gbwt cmp: parse_x.gbwt: No such file or directory t/37_vg_gbwt.t: line 50: 1198385 Illegal instruction (core dumped) vg gbwt -E -o x.ref.gbwt -x x.vg t/37_vg_gbwt.t: line 52: 1198386 Illegal instruction (core dumped) vg index -G x2.ref.gbwt -T x.vg cmp: x.ref.gbwt: No such file or directory t/37_vg_gbwt.t: line 62: 1198390 Illegal instruction (core dumped) vg paths -v x.vg -X -Q _alt > x.alts.gam t/37_vg_gbwt.t: line 63: 1198391 Illegal instruction (core dumped) vg convert -G x.alts.gam x.vg > x.alts.gaf t/37_vg_gbwt.t: line 64: 1198392 Illegal instruction (core dumped) vg gbwt -A -o x.alts.gaf.gbwt -x x.vg x.alts.gaf t/37_vg_gbwt.t: line 66: 1198393 Illegal instruction (core dumped) vg index -F x.alts.gaf -G x2.alts.gaf.gbwt x.vg cmp: x.alts.gaf.gbwt: No such file or directory t/37_vg_gbwt.t: line 70: 1198395 Illegal instruction (core dumped) vg gbwt -A --gam-format -o x.alts.gam.gbwt -x x.vg x.alts.gam cmp: x.alts.gaf.gbwt: No such file or directory t/37_vg_gbwt.t: line 80: 1198399 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a --region x:100-200 > x.part.vg t/37_vg_gbwt.t: line 81: 1198400 Illegal instruction (core dumped) vg gbwt -x x.part.vg -o x.part.gbwt --vcf-region x:100-200 -v small/x.vcf.gz 2> log.txt t/37_vg_gbwt.t: line 84: 1198404 Illegal instruction (core dumped) vg index -G x2.part.gbwt --region x:100-200 -v small/x.vcf.gz x.part.vg 2> log.txt cmp: x.part.gbwt: No such file or directory t/37_vg_gbwt.t: line 93: 1198407 Illegal instruction (core dumped) vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 94: 1198408 Illegal instruction (core dumped) vg gbwt -x y.vg -o y.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 95: 1198409 Illegal instruction (core dumped) vg gbwt -m -o xy.merge.gbwt x.gbwt y.gbwt t/37_vg_gbwt.t: line 97: 1198410 Illegal instruction (core dumped) vg gbwt -f -o xy.fast.gbwt x.gbwt y.gbwt cmp: xy.merge.gbwt: No such file or directory t/37_vg_gbwt.t: line 101: 1198412 Illegal instruction (core dumped) vg gbwt -b --merge-jobs 1 -o xy.parallel.gbwt x.gbwt y.gbwt cmp: xy.merge.gbwt: No such file or directory t/37_vg_gbwt.t: line 105: 1198414 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -o xy.direct.gbwt -v small/xy2.vcf.gz cmp: xy.direct.gbwt: No such file or directory t/37_vg_gbwt.t: line 109: 1198416 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -o xy.multi.gbwt -v --inputs-as-jobs small/xy2_x.vcf.gz small/xy2_y.vcf.gz cmp: xy.direct.gbwt: No such file or directory t/37_vg_gbwt.t: line 115: 1198418 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -o xy.1000gp.gbwt --preset 1000gp -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 129: 1198425 Illegal instruction (core dumped) vg gbwt -E -o xy.contigs.gbwt -x xy.xg t/37_vg_gbwt.t: line 131: 1198426 Illegal instruction (core dumped) vg index -G xy2.contigs.gbwt -T xy.xg cmp: xy.contigs.gbwt: No such file or directory t/37_vg_gbwt.t: line 141: 1198432 Illegal instruction (core dumped) vg gbwt -E --paths-as-samples -o xy.samples.gbwt -x xy.xg t/37_vg_gbwt.t: line 143: 1198433 Illegal instruction (core dumped) vg index -G xy2.samples.gbwt -T --paths-as-samples xy.xg cmp: xy.samples.gbwt: No such file or directory t/37_vg_gbwt.t: line 156: 1198440 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -o xy.gbwt -r xy.ri --num-threads 1 -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 163: 1198442 Illegal instruction (core dumped) vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 167: 1198444 Illegal instruction (core dumped) vg gbwt -m -o x2.gbwt x.gbwt empty.gbwt cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 173: 1198446 Illegal instruction (core dumped) vg gbwt -m -o x2.gbwt empty.gbwt x.gbwt 2> /dev/null cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 179: 1198448 Illegal instruction (core dumped) vg gbwt -f -o x2.gbwt x.gbwt empty.gbwt cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 185: 1198450 Illegal instruction (core dumped) vg gbwt -f -o x2.gbwt empty.gbwt x.gbwt cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 191: 1198452 Illegal instruction (core dumped) vg gbwt -b --merge-jobs 1 -o x2.gbwt x.gbwt empty.gbwt cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 197: 1198454 Illegal instruction (core dumped) vg gbwt -b --merge-jobs 1 -o x2.gbwt empty.gbwt x.gbwt 2> /dev/null cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 206: 1198457 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -o xy.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 207: 1198458 Illegal instruction (core dumped) vg gbwt -E -o xy.ref.gbwt -x xy.xg t/37_vg_gbwt.t: line 208: 1198459 Illegal instruction (core dumped) vg gbwt -m -o xy.both.gbwt xy.gbwt xy.ref.gbwt t/37_vg_gbwt.t: line 212: 1198461 Illegal instruction (core dumped) vg gbwt -R ref -o xy.removed.gbwt xy.both.gbwt t/37_vg_gbwt.t: line 220: 1198464 Illegal instruction (core dumped) vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 221: 1198465 Illegal instruction (core dumped) vg gbwt -e x.extract x.gbwt cat: x.extract: No such file or directory t/37_vg_gbwt.t: line 229: 1198470 Illegal instruction (core dumped) vg gbwt -x x.vg -g x.gg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 231: 1198471 Illegal instruction (core dumped) vg view --extract-tag GBWTGraph x.gg > x.extracted.gg t/37_vg_gbwt.t: line 238: 1198476 Illegal instruction (core dumped) vg gbwt -P -n 16 -x xy.xg -g xy.cover.gg -o xy.cover.gbwt t/37_vg_gbwt.t: line 240: 1198477 Illegal instruction (core dumped) vg view --extract-tag GBWTGraph xy.cover.gg > xy.extracted.gg t/37_vg_gbwt.t: line 251: 1198486 Illegal instruction (core dumped) vg gbwt -x xy-alt.xg -g xy.local.gg -l -n 16 -o xy.local.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 253: 1198487 Illegal instruction (core dumped) vg view --extract-tag GBWTGraph xy.local.gg > xy.extracted.gg t/37_vg_gbwt.t: line 264: 1198496 Illegal instruction (core dumped) vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz t/37_vg_gbwt.t: line 265: 1198497 Illegal instruction (core dumped) vg gbwt -a -n 16 -x xy.xg -g augmented.gg -o augmented.gbwt x.gbwt t/37_vg_gbwt.t: line 267: 1198498 Illegal instruction (core dumped) vg view --extract-tag GBWTGraph augmented.gg > augmented.extracted.gg t/37_vg_gbwt.t ........ 1..91 not ok 1 - chromosome X GBWT with vg gbwt # got: '132' # expected: '0' not ok 2 - chromosome X GBWT with vg index # got: '132' # expected: '0' not ok 3 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 4 - chromosome X VCF parse # got: '132' # expected: '0' not ok 5 - chromosome X GBWT from VCF parse # got: '1' # expected: '0' not ok 6 - identical construction results with vg gbwt and from VCF parse # got: '2' # expected: '0' not ok 7 - unnamed test # got: '2' # expected: 'chromosome X: 2 threads' not ok 8 - unnamed test # got: '1' # expected: 'chromosome X: 1 contig' not ok 9 - unnamed test # got: '2' # expected: 'chromosome X: 2 haplotypes' not ok 10 - unnamed test # got: '1' # expected: 'chromosome X: 1 sample' not ok 11 - chromosome X: 2 thread names # got: '0' # expected: '2' not ok 12 - chromosome X: 1 contig name # got: '0' # expected: '1' not ok 13 - chromosome X: 1 sample name # got: '0' # expected: '1' not ok 14 - chromosome X reference GBWT with vg gbwt # got: '132' # expected: '0' not ok 15 - chromosome X reference GBWT with vg index # got: '132' # expected: '0' not ok 16 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 17 - unnamed test # got: '1' # expected: 'chromosome X reference: 1 thread' not ok 18 - chromosome X GAF with vg gbwt # got: '132' # expected: '0' not ok 19 - chromosome X GAF with vg index # got: '132' # expected: '0' not ok 20 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 21 - chromosome X GAM with vg gbwt # got: '132' # expected: '0' not ok 22 - identical construction results from GAF and GAM # got: '2' # expected: '0' not ok 23 - chromosome X subgraph GBWT with vg gbwt # got: '132' # expected: '0' ok 24 - no warnings about missing variants not ok 25 - chromosome X subgraph GBWT with vg index # got: '132' # expected: '0' not ok 26 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 27 - insertion merging with multiple chromosomes # got: '132' # expected: '0' not ok 28 - fast merging with multiple chromosomes # got: '132' # expected: '0' not ok 29 - identical merging results with the insertion and fast algorithms # got: '2' # expected: '0' not ok 30 - parallel merging with multiple chromosomes # got: '132' # expected: '0' not ok 31 - identical merging results with the insertion and parallel algorithms # got: '2' # expected: '0' not ok 32 - direct construction with multiple chromosomes and a single VCF # got: '132' # expected: '0' not ok 33 - identical results with direct construction and merging # got: '2' # expected: '0' not ok 34 - direct construction with multiple chromosomes and multiple VCFs # got: '132' # expected: '0' not ok 35 - identical construction results with a single VCF and multiple VCFs # got: '2' # expected: '0' not ok 36 - construction preset: 1000gp # got: '132' # expected: '0' not ok 37 - unnamed test # got: '4' # expected: 'multiple chromosomes: 4 threads' not ok 38 - unnamed test # got: '2' # expected: 'multiple chromosomes: 2 contigs' not ok 39 - unnamed test # got: '2' # expected: 'multiple chromosomes: 2 haplotypes' not ok 40 - unnamed test # got: '1' # expected: 'multiple chromosomes: 1 sample' not ok 41 - paths as contigs with vg gbwt # got: '132' # expected: '0' not ok 42 - paths as contigs with vg index # got: '132' # expected: '0' not ok 43 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 44 - unnamed test # got: '2' # expected: 'paths as contigs: 2 threads' not ok 45 - unnamed test # got: '2' # expected: 'paths as contigs: 2 contigs' not ok 46 - unnamed test # got: '1' # expected: 'paths as contigs: 1 haplotype' not ok 47 - unnamed test # got: '1' # expected: 'paths as contigs: 1 sample' not ok 48 - paths as samples with vg gbwt # got: '132' # expected: '0' not ok 49 - paths as samples with vg index # got: '132' # expected: '0' not ok 50 - unnamed test # got: '2' # expected: 'paths as samples: 2 threads' not ok 51 - unnamed test # got: '1' # expected: 'paths as samples: 1 contig' not ok 52 - unnamed test # got: '2' # expected: 'paths as samples: 2 haplotypes' not ok 53 - unnamed test # got: '2' # expected: 'paths as samples: 2 samples' not ok 54 - r-index construction # got: '132' # expected: '0' not ok 55 - normal merging: non-empty + empty # got: '132' # expected: '0' not ok 56 - the index remains unchanged # got: '2' # expected: '0' not ok 57 - normal merging: empty + non-empty # got: '132' # expected: '0' not ok 58 - the index remains unchanged # got: '2' # expected: '0' not ok 59 - fast merging: non-empty + empty # got: '132' # expected: '0' not ok 60 - the index remains unchanged # got: '2' # expected: '0' not ok 61 - fast merging: empty + non-empty # got: '132' # expected: '0' not ok 62 - the index remains unchanged # got: '2' # expected: '0' not ok 63 - parallel merging: non-empty + empty # got: '132' # expected: '0' not ok 64 - the index remains unchanged # got: '2' # expected: '0' not ok 65 - parallel merging: empty + non-empty # got: '132' # expected: '0' not ok 66 - the index remains unchanged # got: '2' # expected: '0' not ok 67 - unnamed test # got: '6' # expected: 'haplotypes and paths: 6 threads' not ok 68 - samples can be removed from a GBWT index # got: '132' # expected: '0' not ok 69 - unnamed test # got: '4' # expected: 'haplotypes only: 4 threads' not ok 70 - threads can be extracted from GBWT # got: '132' # expected: '0' not ok 71 - correct size for the thread file # got: '0' # expected: '121' not ok 72 - GBWTGraph construction was successful # got: '132' # expected: '0' not ok 73 - GBWTGraph was correctly serialized # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '62d451917c5076d7e84a6837dfb836cb' not ok 74 - Path cover GBWTGraph construction was successful # got: '132' # expected: '0' not ok 75 - GBWTGraph was correctly serialized # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'ae6ba365e7e5fac6456f9a5a130aa98f' not ok 76 - unnamed test # got: '32' # expected: 'path cover: 32 threads' not ok 77 - unnamed test # got: '2' # expected: 'path cover: 2 contigs' not ok 78 - unnamed test # got: '16' # expected: 'path cover: 16 haplotypes' not ok 79 - unnamed test # got: '16' # expected: 'path cover: 16 samples' not ok 80 - Local haplotypes GBWTGraph construction was successful # got: '132' # expected: '0' not ok 81 - GBWTGraph was correctly serialized # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'b7b40fb5296ded80cc659cd2300015af' not ok 82 - unnamed test # got: '32' # expected: 'local haplotypes: 32 threads' not ok 83 - unnamed test # got: '2' # expected: 'local haplotypes: 2 contigs' not ok 84 - unnamed test # got: '16' # expected: 'local haplotypes: 16 haplotypes' not ok 85 - unnamed test # got: '16' # expected: 'local haplotypes: 16 samples' not ok 86 - Augmented GBWTGraph construction was successful # got: '132' # expected: '0' not ok 87 - GBWTGraph was correctly serialized # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'b7b40fb5296ded80cc659cd2300015af' not ok 88 - unnamed test # got: '18' # expected: 'augmented: 18 threads' not ok 89 - unnamed test # got: '2' # expected: 'augmented: 2 contigs' not ok 90 - unnamed test # got: '2' # expected: 'augmented: 2 haplotypes' not ok 91 - unnamed test # got: '17' # expected: 'augmented: 17 samples' Failed 90/91 subtests t/38_vg_prune.t: line 12: 1198509 Illegal instruction (core dumped) vg construct -m 32 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/38_vg_prune.t: line 13: 1198510 Illegal instruction (core dumped) vg index -G x.gbwt -v small/xy2.vcf.gz x.vg t/38_vg_prune.t: line 16: 1198511 Illegal instruction (core dumped) vg prune -e 1 x.vg > y.vg t/38_vg_prune.t: line 23: 1198518 Illegal instruction (core dumped) vg prune -e 1 -M 3 x.vg > y.vg t/38_vg_prune.t: line 30: 1198525 Illegal instruction (core dumped) vg prune -r -e 1 x.vg > y.vg t/38_vg_prune.t: line 37: 1198532 Illegal instruction (core dumped) vg prune -u -m x.mapping -g x.gbwt -e 1 x.vg > y.vg t/38_vg_prune.t: line 44: 1198539 Illegal instruction (core dumped) vg prune -u -m x.mapping -e 1 x.vg > y.vg t/38_vg_prune.t: line 54: 1198547 Illegal instruction (core dumped) vg construct -m 1000 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/38_vg_prune.t: line 55: 1198548 Illegal instruction (core dumped) vg construct -m 1000 -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null t/38_vg_prune.t: line 56: 1198549 Illegal instruction (core dumped) vg ids -j -m xy.mapping x.vg y.vg t/38_vg_prune.t: line 57: 1198550 Illegal instruction (core dumped) vg index -G x.gbwt -v small/xy2.vcf.gz x.vg t/38_vg_prune.t: line 58: 1198551 Illegal instruction (core dumped) vg index -G y.gbwt -v small/xy2.vcf.gz y.vg head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t: line 62: 1198555 Illegal instruction (core dumped) vg prune -u -g x.gbwt -e 1 -a -m xy.mapping x.vg > /dev/null head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t: line 64: 1198559 Illegal instruction (core dumped) vg prune -u -g y.gbwt -e 1 -a -m xy.mapping y.vg > /dev/null head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t ....... 1..18 not ok 1 - pruning produces the correct number of components # got: '0' # expected: '5' not ok 2 - unnamed test # got: '51' # expected: 'pruning leaves the correct number of nodes' not ok 3 - unnamed test # got: '51' # expected: 'pruning leaves the correct number of edges' not ok 4 - pruning without high-degree nodes produces the correct number of components # got: '0' # expected: '6' not ok 5 - unnamed test # got: '50' # expected: 'pruning without high-degree nodes leaves the correct number of nodes' not ok 6 - unnamed test # got: '47' # expected: 'pruning without high-degree nodes leaves the correct number of edges' not ok 7 - pruning with path restoring produces the correct number of components # got: '0' # expected: '1' not ok 8 - unnamed test # got: '64' # expected: 'pruning with path restoring leaves the correct number of nodes' not ok 9 - unnamed test # got: '68' # expected: 'pruning with path restoring leaves the correct number of edges' not ok 10 - pruning with path/thread unfolding produces the correct number of components # got: '0' # expected: '1' not ok 11 - unnamed test # got: '80' # expected: 'pruning with path/thread unfolding produces the correct number of nodes' not ok 12 - unnamed test # got: '92' # expected: 'pruning with path/thread unfolding produces the correct number of edges' not ok 13 - pruning with path unfolding produces the correct number of components # got: '0' # expected: '1' not ok 14 - unnamed test # got: '64' # expected: 'pruning with path unfolding produces the correct number of nodes' not ok 15 - unnamed test # got: '68' # expected: 'pruning with path unfolding produces the correct number of edges' not ok 16 - unnamed test # got: '99_0_99_0_' # expected: 'empty mapping starts from the right node id' not ok 17 - unnamed test # got: '99_0_128_0_' # expected: 'the first unfolded graph adds the correct number of nodes to the mapping' not ok 18 - unnamed test # got: '99_0_156_0_' # expected: 'the second unfolded graph adds the correct number of nodes to the mapping' Failed 18/18 subtests t/39_vg_inject.t: line 11: 1198565 Illegal instruction (core dumped) vg construct -r small/x.fa > j.vg t/39_vg_inject.t: line 12: 1198566 Illegal instruction (core dumped) vg index -x j.xg j.vg t/39_vg_inject.t: line 13: 1198567 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/39_vg_inject.t: line 14: 1198568 Illegal instruction (core dumped) vg index -k 11 -g x.gcsa -x x.xg x.vg [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". t/39_vg_inject.t ...... 1..10 not ok 1 - reads are generated # got: '0' # expected: '1000' not ok 2 - vg inject works for all reads included in the original bam # got: '0' # expected: '1000' not ok 3 - vg inject retains read names # got: 'small/x.fa.fastq.000000000 # small/x.fa.fastq.000000001 # small/x.fa.fastq.000000002 # small/x.fa.fastq.000000003 # small/x.fa.fastq.000000004 # small/x.fa.fastq.000000005 # small/x.fa.fastq.000000006 # small/x.fa.fastq.000000007 # small/x.fa.fastq.000000008 # small/x.fa.fastq.000000009 # small/x.fa.fastq.000000010 # small/x.fa.fastq.000000011 # small/x.fa.fastq.000000012 # small/x.fa.fastq.000000013 # small/x.fa.fastq.000000014 # small/x.fa.fastq.000000015 # small/x.fa.fastq.000000016 # small/x.fa.fastq.000000017 # small/x.fa.fastq.000000018 # small/x.fa.fastq.000000019 # small/x.fa.fastq.000000020 # small/x.fa.fastq.000000021 # small/x.fa.fastq.000000022 # small/x.fa.fastq.000000023 # small/x.fa.fastq.000000024 # small/x.fa.fastq.000000025 # small/x.fa.fastq.000000026 # small/x.fa.fastq.000000027 # small/x.fa.fastq.000000028 # small/x.fa.fastq.000000029 # small/x.fa.fastq.000000030 # small/x.fa.fastq.000000031 # small/x.fa.fastq.000000032 # small/x.fa.fastq.000000033 # small/x.fa.fastq.000000034 # small/x.fa.fastq.000000035 # small/x.fa.fastq.000000036 # small/x.fa.fastq.000000037 # small/x.fa.fastq.000000038 # small/x.fa.fastq.000000039 # small/x.fa.fastq.000000040 # small/x.fa.fastq.000000041 # small/x.fa.fastq.000000042 # small/x.fa.fastq.000000043 # small/x.fa.fastq.000000044 # small/x.fa.fastq.000000045 # small/x.fa.fastq.000000046 # small/x.fa.fastq.000000047 # small/x.fa.fastq.000000048 # small/x.fa.fastq.000000049 # small/x.fa.fastq.000000050 # small/x.fa.fastq.000000051 # small/x.fa.fastq.000000052 # small/x.fa.fastq.000000053 # small/x.fa.fastq.000000054 # small/x.fa.fastq.000000055 # small/x.fa.fastq.000000056 # small/x.fa.fastq.000000057 # small/x.fa.fastq.000000058 # small/x.fa.fastq.000000059 # small/x.fa.fastq.000000060 # small/x.fa.fastq.000000061 # small/x.fa.fastq.000000062 # small/x.fa.fastq.000000063 # small/x.fa.fastq.000000064 # small/x.fa.fastq.000000065 # small/x.fa.fastq.000000066 # small/x.fa.fastq.000000067 # small/x.fa.fastq.000000068 # small/x.fa.fastq.000000069 # small/x.fa.fastq.000000070 # small/x.fa.fastq.000000071 # small/x.fa.fastq.000000072 # small/x.fa.fastq.000000073 # small/x.fa.fastq.000000074 # small/x.fa.fastq.000000075 # small/x.fa.fastq.000000076 # small/x.fa.fastq.000000077 # small/x.fa.fastq.000000078 # small/x.fa.fastq.000000079 # small/x.fa.fastq.000000080 # small/x.fa.fastq.000000081 # small/x.fa.fastq.000000082 # small/x.fa.fastq.000000083 # small/x.fa.fastq.000000084 # small/x.fa.fastq.000000085 # small/x.fa.fastq.000000086 # small/x.fa.fastq.000000087 # small/x.fa.fastq.000000088 # small/x.fa.fastq.000000089 # small/x.fa.fastq.000000090 # small/x.fa.fastq.000000091 # small/x.fa.fastq.000000092 # small/x.fa.fastq.000000093 # small/x.fa.fastq.000000094 # small/x.fa.fastq.000000095 # small/x.fa.fastq.000000096 # small/x.fa.fastq.000000097 # small/x.fa.fastq.000000098 # small/x.fa.fastq.000000099 # small/x.fa.fastq.000000100 # small/x.fa.fastq.000000101 # small/x.fa.fastq.000000102 # small/x.fa.fastq.000000103 # small/x.fa.fastq.000000104 # small/x.fa.fastq.000000105 # small/x.fa.fastq.000000106 # small/x.fa.fastq.000000107 # small/x.fa.fastq.000000108 # small/x.fa.fastq.000000109 # small/x.fa.fastq.000000110 # small/x.fa.fastq.000000111 # small/x.fa.fastq.000000112 # small/x.fa.fastq.000000113 # small/x.fa.fastq.000000114 # small/x.fa.fastq.000000115 # small/x.fa.fastq.000000116 # small/x.fa.fastq.000000117 # small/x.fa.fastq.000000118 # small/x.fa.fastq.000000119 # small/x.fa.fastq.000000120 # small/x.fa.fastq.000000121 # small/x.fa.fastq.000000122 # small/x.fa.fastq.000000123 # small/x.fa.fastq.000000124 # small/x.fa.fastq.000000125 # small/x.fa.fastq.000000126 # small/x.fa.fastq.000000127 # small/x.fa.fastq.000000128 # small/x.fa.fastq.000000129 # small/x.fa.fastq.000000130 # small/x.fa.fastq.000000131 # small/x.fa.fastq.000000132 # small/x.fa.fastq.000000133 # small/x.fa.fastq.000000134 # small/x.fa.fastq.000000135 # small/x.fa.fastq.000000136 # small/x.fa.fastq.000000137 # small/x.fa.fastq.000000138 # small/x.fa.fastq.000000139 # small/x.fa.fastq.000000140 # small/x.fa.fastq.000000141 # small/x.fa.fastq.000000142 # small/x.fa.fastq.000000143 # small/x.fa.fastq.000000144 # small/x.fa.fastq.000000145 # small/x.fa.fastq.000000146 # small/x.fa.fastq.000000147 # small/x.fa.fastq.000000148 # small/x.fa.fastq.000000149 # small/x.fa.fastq.000000150 # small/x.fa.fastq.000000151 # small/x.fa.fastq.000000152 # small/x.fa.fastq.000000153 # small/x.fa.fastq.000000154 # small/x.fa.fastq.000000155 # small/x.fa.fastq.000000156 # small/x.fa.fastq.000000157 # small/x.fa.fastq.000000158 # small/x.fa.fastq.000000159 # small/x.fa.fastq.000000160 # small/x.fa.fastq.000000161 # small/x.fa.fastq.000000162 # small/x.fa.fastq.000000163 # small/x.fa.fastq.000000164 # small/x.fa.fastq.000000165 # small/x.fa.fastq.000000166 # small/x.fa.fastq.000000167 # small/x.fa.fastq.000000168 # small/x.fa.fastq.000000169 # small/x.fa.fastq.000000170 # small/x.fa.fastq.000000171 # small/x.fa.fastq.000000172 # small/x.fa.fastq.000000173 # small/x.fa.fastq.000000174 # small/x.fa.fastq.000000175 # small/x.fa.fastq.000000176 # small/x.fa.fastq.000000177 # small/x.fa.fastq.000000178 # small/x.fa.fastq.000000179 # small/x.fa.fastq.000000180 # small/x.fa.fastq.000000181 # small/x.fa.fastq.000000182 # small/x.fa.fastq.000000183 # small/x.fa.fastq.000000184 # small/x.fa.fastq.000000185 # small/x.fa.fastq.000000186 # small/x.fa.fastq.000000187 # small/x.fa.fastq.000000188 # small/x.fa.fastq.000000189 # small/x.fa.fastq.000000190 # small/x.fa.fastq.000000191 # small/x.fa.fastq.000000192 # small/x.fa.fastq.000000193 # small/x.fa.fastq.000000194 # small/x.fa.fastq.000000195 # small/x.fa.fastq.000000196 # small/x.fa.fastq.000000197 # small/x.fa.fastq.000000198 # small/x.fa.fastq.000000199 # small/x.fa.fastq.000000200 # small/x.fa.fastq.000000201 # small/x.fa.fastq.000000202 # small/x.fa.fastq.000000203 # small/x.fa.fastq.000000204 # small/x.fa.fastq.000000205 # small/x.fa.fastq.000000206 # small/x.fa.fastq.000000207 # small/x.fa.fastq.000000208 # small/x.fa.fastq.000000209 # small/x.fa.fastq.000000210 # small/x.fa.fastq.000000211 # small/x.fa.fastq.000000212 # small/x.fa.fastq.000000213 # small/x.fa.fastq.000000214 # small/x.fa.fastq.000000215 # small/x.fa.fastq.000000216 # small/x.fa.fastq.000000217 # small/x.fa.fastq.000000218 # small/x.fa.fastq.000000219 # small/x.fa.fastq.000000220 # small/x.fa.fastq.000000221 # small/x.fa.fastq.000000222 # small/x.fa.fastq.000000223 # small/x.fa.fastq.000000224 # small/x.fa.fastq.000000225 # small/x.fa.fastq.000000226 # small/x.fa.fastq.000000227 # small/x.fa.fastq.000000228 # small/x.fa.fastq.000000229 # small/x.fa.fastq.000000230 # small/x.fa.fastq.000000231 # small/x.fa.fastq.000000232 # small/x.fa.fastq.000000233 # small/x.fa.fastq.000000234 # small/x.fa.fastq.000000235 # small/x.fa.fastq.000000236 # small/x.fa.fastq.000000237 # small/x.fa.fastq.000000238 # small/x.fa.fastq.000000239 # small/x.fa.fastq.000000240 # small/x.fa.fastq.000000241 # small/x.fa.fastq.000000242 # small/x.fa.fastq.000000243 # small/x.fa.fastq.000000244 # small/x.fa.fastq.000000245 # small/x.fa.fastq.000000246 # small/x.fa.fastq.000000247 # small/x.fa.fastq.000000248 # small/x.fa.fastq.000000249 # small/x.fa.fastq.000000250 # small/x.fa.fastq.000000251 # small/x.fa.fastq.000000252 # small/x.fa.fastq.000000253 # small/x.fa.fastq.000000254 # small/x.fa.fastq.000000255 # small/x.fa.fastq.000000256 # small/x.fa.fastq.000000257 # small/x.fa.fastq.000000258 # small/x.fa.fastq.000000259 # small/x.fa.fastq.000000260 # small/x.fa.fastq.000000261 # small/x.fa.fastq.000000262 # small/x.fa.fastq.000000263 # small/x.fa.fastq.000000264 # small/x.fa.fastq.000000265 # small/x.fa.fastq.000000266 # small/x.fa.fastq.000000267 # small/x.fa.fastq.000000268 # small/x.fa.fastq.000000269 # small/x.fa.fastq.000000270 # small/x.fa.fastq.000000271 # small/x.fa.fastq.000000272 # small/x.fa.fastq.000000273 # small/x.fa.fastq.000000274 # small/x.fa.fastq.000000275 # small/x.fa.fastq.000000276 # small/x.fa.fastq.000000277 # small/x.fa.fastq.000000278 # small/x.fa.fastq.000000279 # small/x.fa.fastq.000000280 # small/x.fa.fastq.000000281 # small/x.fa.fastq.000000282 # small/x.fa.fastq.000000283 # small/x.fa.fastq.000000284 # small/x.fa.fastq.000000285 # small/x.fa.fastq.000000286 # small/x.fa.fastq.000000287 # small/x.fa.fastq.000000288 # small/x.fa.fastq.000000289 # small/x.fa.fastq.000000290 # small/x.fa.fastq.000000291 # small/x.fa.fastq.000000292 # small/x.fa.fastq.000000293 # small/x.fa.fastq.000000294 # small/x.fa.fastq.000000295 # small/x.fa.fastq.000000296 # small/x.fa.fastq.000000297 # small/x.fa.fastq.000000298 # small/x.fa.fastq.000000299 # small/x.fa.fastq.000000300 # small/x.fa.fastq.000000301 # small/x.fa.fastq.000000302 # small/x.fa.fastq.000000303 # small/x.fa.fastq.000000304 # small/x.fa.fastq.000000305 # small/x.fa.fastq.000000306 # small/x.fa.fastq.000000307 # small/x.fa.fastq.000000308 # small/x.fa.fastq.000000309 # small/x.fa.fastq.000000310 # small/x.fa.fastq.000000311 # small/x.fa.fastq.000000312 # small/x.fa.fastq.000000313 # small/x.fa.fastq.000000314 # small/x.fa.fastq.000000315 # small/x.fa.fastq.000000316 # small/x.fa.fastq.000000317 # small/x.fa.fastq.000000318 # small/x.fa.fastq.000000319 # small/x.fa.fastq.000000320 # small/x.fa.fastq.000000321 # small/x.fa.fastq.000000322 # small/x.fa.fastq.000000323 # small/x.fa.fastq.000000324 # small/x.fa.fastq.000000325 # small/x.fa.fastq.000000326 # small/x.fa.fastq.000000327 # small/x.fa.fastq.000000328 # small/x.fa.fastq.000000329 # small/x.fa.fastq.000000330 # small/x.fa.fastq.000000331 # small/x.fa.fastq.000000332 # small/x.fa.fastq.000000333 # small/x.fa.fastq.000000334 # small/x.fa.fastq.000000335 # small/x.fa.fastq.000000336 # small/x.fa.fastq.000000337 # small/x.fa.fastq.000000338 # small/x.fa.fastq.000000339 # small/x.fa.fastq.000000340 # small/x.fa.fastq.000000341 # small/x.fa.fastq.000000342 # small/x.fa.fastq.000000343 # small/x.fa.fastq.000000344 # small/x.fa.fastq.000000345 # small/x.fa.fastq.000000346 # small/x.fa.fastq.000000347 # small/x.fa.fastq.000000348 # small/x.fa.fastq.000000349 # small/x.fa.fastq.000000350 # small/x.fa.fastq.000000351 # small/x.fa.fastq.000000352 # small/x.fa.fastq.000000353 # small/x.fa.fastq.000000354 # small/x.fa.fastq.000000355 # small/x.fa.fastq.000000356 # small/x.fa.fastq.000000357 # small/x.fa.fastq.000000358 # small/x.fa.fastq.000000359 # small/x.fa.fastq.000000360 # small/x.fa.fastq.000000361 # small/x.fa.fastq.000000362 # small/x.fa.fastq.000000363 # small/x.fa.fastq.000000364 # small/x.fa.fastq.000000365 # small/x.fa.fastq.000000366 # small/x.fa.fastq.000000367 # small/x.fa.fastq.000000368 # small/x.fa.fastq.000000369 # small/x.fa.fastq.000000370 # small/x.fa.fastq.000000371 # small/x.fa.fastq.000000372 # small/x.fa.fastq.000000373 # small/x.fa.fastq.000000374 # small/x.fa.fastq.000000375 # small/x.fa.fastq.000000376 # small/x.fa.fastq.000000377 # small/x.fa.fastq.000000378 # small/x.fa.fastq.000000379 # small/x.fa.fastq.000000380 # small/x.fa.fastq.000000381 # small/x.fa.fastq.000000382 # small/x.fa.fastq.000000383 # small/x.fa.fastq.000000384 # small/x.fa.fastq.000000385 # small/x.fa.fastq.000000386 # small/x.fa.fastq.000000387 # small/x.fa.fastq.000000388 # small/x.fa.fastq.000000389 # small/x.fa.fastq.000000390 # small/x.fa.fastq.000000391 # small/x.fa.fastq.000000392 # small/x.fa.fastq.000000393 # small/x.fa.fastq.000000394 # small/x.fa.fastq.000000395 # small/x.fa.fastq.000000396 # small/x.fa.fastq.000000397 # small/x.fa.fastq.000000398 # small/x.fa.fastq.000000399 # small/x.fa.fastq.000000400 # small/x.fa.fastq.000000401 # small/x.fa.fastq.000000402 # small/x.fa.fastq.000000403 # small/x.fa.fastq.000000404 # small/x.fa.fastq.000000405 # small/x.fa.fastq.000000406 # small/x.fa.fastq.000000407 # small/x.fa.fastq.000000408 # small/x.fa.fastq.000000409 # small/x.fa.fastq.000000410 # small/x.fa.fastq.000000411 # small/x.fa.fastq.000000412 # small/x.fa.fastq.000000413 # small/x.fa.fastq.000000414 # small/x.fa.fastq.000000415 # small/x.fa.fastq.000000416 # small/x.fa.fastq.000000417 # small/x.fa.fastq.000000418 # small/x.fa.fastq.000000419 # small/x.fa.fastq.000000420 # small/x.fa.fastq.000000421 # small/x.fa.fastq.000000422 # small/x.fa.fastq.000000423 # small/x.fa.fastq.000000424 # small/x.fa.fastq.000000425 # small/x.fa.fastq.000000426 # small/x.fa.fastq.000000427 # small/x.fa.fastq.000000428 # small/x.fa.fastq.000000429 # small/x.fa.fastq.000000430 # small/x.fa.fastq.000000431 # 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small/x.fa.fastq.000000704 # small/x.fa.fastq.000000705 # small/x.fa.fastq.000000706 # small/x.fa.fastq.000000707 # small/x.fa.fastq.000000708 # small/x.fa.fastq.000000709 # small/x.fa.fastq.000000710 # small/x.fa.fastq.000000711 # small/x.fa.fastq.000000712 # small/x.fa.fastq.000000713 # small/x.fa.fastq.000000714 # small/x.fa.fastq.000000715 # small/x.fa.fastq.000000716 # small/x.fa.fastq.000000717 # small/x.fa.fastq.000000718 # small/x.fa.fastq.000000719 # small/x.fa.fastq.000000720 # small/x.fa.fastq.000000721 # small/x.fa.fastq.000000722 # small/x.fa.fastq.000000723 # small/x.fa.fastq.000000724 # small/x.fa.fastq.000000725 # small/x.fa.fastq.000000726 # small/x.fa.fastq.000000727 # small/x.fa.fastq.000000728 # small/x.fa.fastq.000000729 # small/x.fa.fastq.000000730 # small/x.fa.fastq.000000731 # small/x.fa.fastq.000000732 # small/x.fa.fastq.000000733 # small/x.fa.fastq.000000734 # small/x.fa.fastq.000000735 # small/x.fa.fastq.000000736 # small/x.fa.fastq.000000737 # small/x.fa.fastq.000000738 # small/x.fa.fastq.000000739 # small/x.fa.fastq.000000740 # small/x.fa.fastq.000000741 # small/x.fa.fastq.000000742 # small/x.fa.fastq.000000743 # small/x.fa.fastq.000000744 # small/x.fa.fastq.000000745 # small/x.fa.fastq.000000746 # small/x.fa.fastq.000000747 # small/x.fa.fastq.000000748 # small/x.fa.fastq.000000749 # small/x.fa.fastq.000000750 # small/x.fa.fastq.000000751 # small/x.fa.fastq.000000752 # small/x.fa.fastq.000000753 # small/x.fa.fastq.000000754 # small/x.fa.fastq.000000755 # small/x.fa.fastq.000000756 # small/x.fa.fastq.000000757 # small/x.fa.fastq.000000758 # small/x.fa.fastq.000000759 # small/x.fa.fastq.000000760 # small/x.fa.fastq.000000761 # small/x.fa.fastq.000000762 # small/x.fa.fastq.000000763 # small/x.fa.fastq.000000764 # small/x.fa.fastq.000000765 # small/x.fa.fastq.000000766 # small/x.fa.fastq.000000767 # small/x.fa.fastq.000000768 # small/x.fa.fastq.000000769 # small/x.fa.fastq.000000770 # small/x.fa.fastq.000000771 # small/x.fa.fastq.000000772 # small/x.fa.fastq.000000773 # small/x.fa.fastq.000000774 # small/x.fa.fastq.000000775 # small/x.fa.fastq.000000776 # small/x.fa.fastq.000000777 # small/x.fa.fastq.000000778 # small/x.fa.fastq.000000779 # small/x.fa.fastq.000000780 # small/x.fa.fastq.000000781 # small/x.fa.fastq.000000782 # small/x.fa.fastq.000000783 # small/x.fa.fastq.000000784 # small/x.fa.fastq.000000785 # small/x.fa.fastq.000000786 # small/x.fa.fastq.000000787 # small/x.fa.fastq.000000788 # small/x.fa.fastq.000000789 # small/x.fa.fastq.000000790 # small/x.fa.fastq.000000791 # small/x.fa.fastq.000000792 # small/x.fa.fastq.000000793 # small/x.fa.fastq.000000794 # small/x.fa.fastq.000000795 # small/x.fa.fastq.000000796 # small/x.fa.fastq.000000797 # small/x.fa.fastq.000000798 # small/x.fa.fastq.000000799 # small/x.fa.fastq.000000800 # small/x.fa.fastq.000000801 # small/x.fa.fastq.000000802 # small/x.fa.fastq.000000803 # small/x.fa.fastq.000000804 # small/x.fa.fastq.000000805 # small/x.fa.fastq.000000806 # small/x.fa.fastq.000000807 # small/x.fa.fastq.000000808 # small/x.fa.fastq.000000809 # small/x.fa.fastq.000000810 # small/x.fa.fastq.000000811 # small/x.fa.fastq.000000812 # small/x.fa.fastq.000000813 # small/x.fa.fastq.000000814 # small/x.fa.fastq.000000815 # small/x.fa.fastq.000000816 # small/x.fa.fastq.000000817 # small/x.fa.fastq.000000818 # small/x.fa.fastq.000000819 # small/x.fa.fastq.000000820 # small/x.fa.fastq.000000821 # small/x.fa.fastq.000000822 # small/x.fa.fastq.000000823 # small/x.fa.fastq.000000824 # small/x.fa.fastq.000000825 # small/x.fa.fastq.000000826 # small/x.fa.fastq.000000827 # small/x.fa.fastq.000000828 # small/x.fa.fastq.000000829 # small/x.fa.fastq.000000830 # small/x.fa.fastq.000000831 # small/x.fa.fastq.000000832 # small/x.fa.fastq.000000833 # small/x.fa.fastq.000000834 # small/x.fa.fastq.000000835 # small/x.fa.fastq.000000836 # small/x.fa.fastq.000000837 # small/x.fa.fastq.000000838 # small/x.fa.fastq.000000839 # small/x.fa.fastq.000000840 # small/x.fa.fastq.000000841 # small/x.fa.fastq.000000842 # small/x.fa.fastq.000000843 # small/x.fa.fastq.000000844 # small/x.fa.fastq.000000845 # small/x.fa.fastq.000000846 # small/x.fa.fastq.000000847 # small/x.fa.fastq.000000848 # small/x.fa.fastq.000000849 # small/x.fa.fastq.000000850 # small/x.fa.fastq.000000851 # small/x.fa.fastq.000000852 # small/x.fa.fastq.000000853 # small/x.fa.fastq.000000854 # small/x.fa.fastq.000000855 # small/x.fa.fastq.000000856 # small/x.fa.fastq.000000857 # small/x.fa.fastq.000000858 # small/x.fa.fastq.000000859 # small/x.fa.fastq.000000860 # small/x.fa.fastq.000000861 # small/x.fa.fastq.000000862 # small/x.fa.fastq.000000863 # small/x.fa.fastq.000000864 # small/x.fa.fastq.000000865 # small/x.fa.fastq.000000866 # small/x.fa.fastq.000000867 # small/x.fa.fastq.000000868 # small/x.fa.fastq.000000869 # small/x.fa.fastq.000000870 # small/x.fa.fastq.000000871 # small/x.fa.fastq.000000872 # small/x.fa.fastq.000000873 # small/x.fa.fastq.000000874 # small/x.fa.fastq.000000875 # small/x.fa.fastq.000000876 # small/x.fa.fastq.000000877 # small/x.fa.fastq.000000878 # small/x.fa.fastq.000000879 # small/x.fa.fastq.000000880 # small/x.fa.fastq.000000881 # small/x.fa.fastq.000000882 # small/x.fa.fastq.000000883 # small/x.fa.fastq.000000884 # small/x.fa.fastq.000000885 # small/x.fa.fastq.000000886 # small/x.fa.fastq.000000887 # small/x.fa.fastq.000000888 # small/x.fa.fastq.000000889 # small/x.fa.fastq.000000890 # small/x.fa.fastq.000000891 # small/x.fa.fastq.000000892 # small/x.fa.fastq.000000893 # small/x.fa.fastq.000000894 # small/x.fa.fastq.000000895 # small/x.fa.fastq.000000896 # small/x.fa.fastq.000000897 # small/x.fa.fastq.000000898 # small/x.fa.fastq.000000899 # small/x.fa.fastq.000000900 # small/x.fa.fastq.000000901 # small/x.fa.fastq.000000902 # small/x.fa.fastq.000000903 # small/x.fa.fastq.000000904 # small/x.fa.fastq.000000905 # small/x.fa.fastq.000000906 # small/x.fa.fastq.000000907 # small/x.fa.fastq.000000908 # small/x.fa.fastq.000000909 # small/x.fa.fastq.000000910 # small/x.fa.fastq.000000911 # small/x.fa.fastq.000000912 # small/x.fa.fastq.000000913 # small/x.fa.fastq.000000914 # small/x.fa.fastq.000000915 # small/x.fa.fastq.000000916 # small/x.fa.fastq.000000917 # small/x.fa.fastq.000000918 # small/x.fa.fastq.000000919 # small/x.fa.fastq.000000920 # small/x.fa.fastq.000000921 # small/x.fa.fastq.000000922 # small/x.fa.fastq.000000923 # small/x.fa.fastq.000000924 # small/x.fa.fastq.000000925 # small/x.fa.fastq.000000926 # small/x.fa.fastq.000000927 # small/x.fa.fastq.000000928 # small/x.fa.fastq.000000929 # small/x.fa.fastq.000000930 # small/x.fa.fastq.000000931 # small/x.fa.fastq.000000932 # small/x.fa.fastq.000000933 # small/x.fa.fastq.000000934 # small/x.fa.fastq.000000935 # small/x.fa.fastq.000000936 # small/x.fa.fastq.000000937 # small/x.fa.fastq.000000938 # small/x.fa.fastq.000000939 # small/x.fa.fastq.000000940 # small/x.fa.fastq.000000941 # small/x.fa.fastq.000000942 # small/x.fa.fastq.000000943 # small/x.fa.fastq.000000944 # small/x.fa.fastq.000000945 # small/x.fa.fastq.000000946 # small/x.fa.fastq.000000947 # small/x.fa.fastq.000000948 # small/x.fa.fastq.000000949 # small/x.fa.fastq.000000950 # small/x.fa.fastq.000000951 # small/x.fa.fastq.000000952 # small/x.fa.fastq.000000953 # small/x.fa.fastq.000000954 # small/x.fa.fastq.000000955 # small/x.fa.fastq.000000956 # small/x.fa.fastq.000000957 # small/x.fa.fastq.000000958 # small/x.fa.fastq.000000959 # small/x.fa.fastq.000000960 # small/x.fa.fastq.000000961 # small/x.fa.fastq.000000962 # small/x.fa.fastq.000000963 # small/x.fa.fastq.000000964 # small/x.fa.fastq.000000965 # small/x.fa.fastq.000000966 # small/x.fa.fastq.000000967 # small/x.fa.fastq.000000968 # small/x.fa.fastq.000000969 # small/x.fa.fastq.000000970 # small/x.fa.fastq.000000971 # small/x.fa.fastq.000000972 # small/x.fa.fastq.000000973 # small/x.fa.fastq.000000974 # small/x.fa.fastq.000000975 # small/x.fa.fastq.000000976 # small/x.fa.fastq.000000977 # small/x.fa.fastq.000000978 # small/x.fa.fastq.000000979 # small/x.fa.fastq.000000980 # small/x.fa.fastq.000000981 # small/x.fa.fastq.000000982 # small/x.fa.fastq.000000983 # small/x.fa.fastq.000000984 # small/x.fa.fastq.000000985 # small/x.fa.fastq.000000986 # small/x.fa.fastq.000000987 # small/x.fa.fastq.000000988 # small/x.fa.fastq.000000989 # small/x.fa.fastq.000000990 # small/x.fa.fastq.000000991 # small/x.fa.fastq.000000992 # small/x.fa.fastq.000000993 # small/x.fa.fastq.000000994 # small/x.fa.fastq.000000995 # small/x.fa.fastq.000000996 # small/x.fa.fastq.000000997 # small/x.fa.fastq.000000998 # small/x.fa.fastq.000000999' # expected: '' not ok 4 - vg inject works perfectly for the position of alignment in the simple graph # got: '1 # 1 # 1 # 3 # 3 # 4 # 4 # 4 # 5 # 7 # 7 # 8 # 8 # 8 # 9 # 11 # 11 # 12 # 12 # 12 # 17 # 17 # 17 # 17 # 17 # 20 # 20 # 20 # 21 # 21 # 25 # 25 # 25 # 31 # 31 # 32 # 33 # 35 # 37 # 40 # 41 # 42 # 45 # 45 # 46 # 48 # 48 # 48 # 48 # 49 # 49 # 50 # 51 # 52 # 52 # 53 # 53 # 53 # 53 # 55 # 56 # 56 # 58 # 58 # 59 # 60 # 60 # 62 # 62 # 64 # 64 # 65 # 66 # 68 # 69 # 69 # 70 # 70 # 70 # 70 # 70 # 71 # 72 # 74 # 75 # 77 # 77 # 77 # 78 # 78 # 78 # 81 # 82 # 83 # 84 # 85 # 86 # 87 # 87 # 87 # 88 # 88 # 88 # 89 # 90 # 90 # 93 # 93 # 94 # 96 # 96 # 97 # 99 # 99 # 100 # 101 # 101 # 102 # 102 # 102 # 102 # 103 # 103 # 104 # 105 # 105 # 106 # 106 # 106 # 107 # 108 # 113 # 113 # 115 # 116 # 116 # 119 # 119 # 120 # 120 # 122 # 123 # 124 # 125 # 125 # 126 # 126 # 127 # 127 # 127 # 128 # 128 # 129 # 130 # 130 # 131 # 131 # 131 # 132 # 134 # 134 # 135 # 136 # 136 # 137 # 137 # 137 # 139 # 140 # 141 # 142 # 142 # 142 # 143 # 143 # 144 # 144 # 145 # 145 # 146 # 147 # 147 # 149 # 150 # 153 # 153 # 154 # 154 # 155 # 156 # 156 # 156 # 157 # 158 # 158 # 158 # 158 # 164 # 164 # 164 # 164 # 165 # 166 # 167 # 167 # 167 # 167 # 168 # 168 # 169 # 170 # 171 # 172 # 172 # 173 # 174 # 175 # 175 # 175 # 177 # 177 # 177 # 178 # 178 # 178 # 178 # 180 # 182 # 183 # 183 # 184 # 184 # 186 # 187 # 188 # 189 # 191 # 193 # 194 # 195 # 197 # 197 # 197 # 197 # 198 # 200 # 200 # 201 # 204 # 205 # 205 # 206 # 207 # 208 # 209 # 210 # 213 # 214 # 214 # 215 # 215 # 216 # 217 # 218 # 218 # 219 # 219 # 219 # 221 # 224 # 224 # 224 # 229 # 229 # 232 # 232 # 232 # 233 # 234 # 234 # 234 # 234 # 237 # 237 # 237 # 238 # 239 # 240 # 240 # 243 # 244 # 245 # 246 # 247 # 250 # 251 # 253 # 253 # 255 # 258 # 258 # 260 # 262 # 265 # 266 # 267 # 268 # 268 # 270 # 270 # 270 # 272 # 273 # 273 # 274 # 274 # 274 # 275 # 276 # 276 # 277 # 277 # 280 # 282 # 283 # 284 # 285 # 285 # 286 # 287 # 287 # 288 # 288 # 289 # 290 # 290 # 291 # 291 # 291 # 291 # 293 # 294 # 294 # 297 # 297 # 298 # 298 # 298 # 300 # 300 # 304 # 306 # 306 # 306 # 307 # 308 # 308 # 308 # 309 # 309 # 310 # 311 # 311 # 312 # 312 # 312 # 313 # 313 # 313 # 314 # 314 # 314 # 315 # 316 # 317 # 319 # 320 # 322 # 323 # 323 # 325 # 325 # 326 # 327 # 332 # 334 # 334 # 334 # 334 # 335 # 336 # 336 # 339 # 339 # 340 # 343 # 344 # 344 # 344 # 345 # 345 # 347 # 347 # 350 # 350 # 351 # 353 # 357 # 357 # 357 # 358 # 358 # 359 # 363 # 363 # 364 # 365 # 365 # 366 # 366 # 367 # 370 # 372 # 373 # 373 # 373 # 375 # 375 # 377 # 379 # 379 # 380 # 380 # 381 # 383 # 385 # 386 # 387 # 389 # 390 # 390 # 391 # 394 # 396 # 399 # 399 # 400 # 400 # 401 # 403 # 403 # 404 # 404 # 404 # 405 # 406 # 406 # 407 # 407 # 408 # 411 # 412 # 412 # 414 # 414 # 415 # 415 # 417 # 418 # 421 # 423 # 425 # 425 # 425 # 425 # 425 # 425 # 425 # 426 # 426 # 427 # 427 # 427 # 428 # 429 # 429 # 430 # 430 # 430 # 430 # 431 # 432 # 433 # 434 # 434 # 435 # 436 # 439 # 440 # 441 # 442 # 443 # 447 # 447 # 448 # 449 # 449 # 450 # 451 # 451 # 452 # 453 # 453 # 453 # 454 # 455 # 455 # 456 # 457 # 458 # 458 # 460 # 460 # 460 # 460 # 462 # 462 # 464 # 464 # 465 # 465 # 466 # 466 # 466 # 467 # 468 # 470 # 471 # 471 # 471 # 471 # 471 # 472 # 473 # 473 # 473 # 474 # 477 # 477 # 478 # 478 # 478 # 480 # 480 # 481 # 482 # 483 # 483 # 483 # 484 # 484 # 484 # 487 # 488 # 490 # 491 # 492 # 493 # 493 # 493 # 494 # 494 # 495 # 497 # 500 # 500 # 501 # 501 # 502 # 503 # 504 # 505 # 506 # 506 # 508 # 508 # 510 # 511 # 514 # 515 # 516 # 516 # 518 # 520 # 521 # 522 # 522 # 523 # 523 # 525 # 525 # 525 # 526 # 527 # 527 # 528 # 530 # 530 # 531 # 532 # 533 # 535 # 537 # 537 # 537 # 538 # 539 # 542 # 544 # 545 # 546 # 546 # 547 # 549 # 549 # 551 # 551 # 552 # 552 # 552 # 553 # 554 # 554 # 556 # 557 # 558 # 558 # 560 # 561 # 563 # 565 # 565 # 566 # 567 # 567 # 569 # 569 # 569 # 570 # 571 # 572 # 572 # 572 # 572 # 573 # 575 # 577 # 578 # 579 # 581 # 582 # 584 # 584 # 585 # 585 # 588 # 589 # 590 # 593 # 593 # 595 # 596 # 597 # 598 # 599 # 600 # 600 # 600 # 600 # 601 # 601 # 602 # 602 # 603 # 604 # 605 # 605 # 606 # 608 # 608 # 608 # 609 # 611 # 612 # 612 # 613 # 613 # 614 # 614 # 615 # 615 # 615 # 616 # 618 # 618 # 619 # 619 # 620 # 620 # 620 # 622 # 625 # 625 # 626 # 626 # 627 # 628 # 629 # 629 # 630 # 630 # 630 # 631 # 632 # 632 # 634 # 634 # 634 # 636 # 636 # 636 # 637 # 637 # 639 # 639 # 639 # 641 # 642 # 642 # 644 # 644 # 645 # 649 # 650 # 650 # 651 # 654 # 655 # 656 # 656 # 657 # 658 # 660 # 661 # 661 # 663 # 667 # 668 # 668 # 671 # 672 # 674 # 674 # 674 # 675 # 676 # 676 # 676 # 676 # 677 # 677 # 680 # 681 # 683 # 684 # 684 # 687 # 688 # 690 # 692 # 693 # 693 # 693 # 696 # 697 # 697 # 700 # 700 # 701 # 702 # 702 # 702 # 703 # 703 # 704 # 704 # 704 # 704 # 705 # 706 # 706 # 707 # 707 # 711 # 713 # 713 # 714 # 718 # 720 # 722 # 723 # 724 # 724 # 724 # 725 # 726 # 726 # 726 # 728 # 729 # 729 # 730 # 733 # 734 # 734 # 735 # 738 # 738 # 738 # 741 # 743 # 746 # 747 # 749 # 751 # 752 # 752 # 753 # 754 # 755 # 756 # 758 # 758 # 759 # 759 # 760 # 761 # 761 # 762 # 763 # 763 # 764 # 765 # 767 # 767 # 768 # 769 # 770 # 770 # 770 # 771 # 771 # 771 # 775 # 776 # 776 # 777 # 779 # 779 # 779 # 779 # 781 # 781 # 782 # 785 # 787 # 787 # 787 # 788 # 789 # 789 # 790 # 790 # 791 # 791 # 792 # 792 # 792 # 793 # 793 # 793 # 794 # 796 # 796 # 802 # 806 # 806 # 807 # 808 # 809 # 809 # 809 # 810 # 810 # 812 # 813 # 818 # 825 # 825 # 826 # 826 # 827 # 827 # 828 # 829 # 830 # 830 # 834 # 834 # 835 # 835 # 836 # 837 # 841 # 844 # 845 # 845 # 845 # 845 # 846 # 846 # 850 # 850 # 852 # 853 # 853 # 854 # 855 # 856 # 858 # 859 # 860 # 861 # 862 # 862 # 863 # 864 # 866 # 869 # 870 # 870 # 871 # 873 # 874 # 874 # 876 # 877 # 877 # 877 # 877 # 879 # 881 # 882 # 883 # 884 # 885 # 885 # 885 # 886 # 887 # 888 # 889 # 889 # 889 # 889 # 889 # 890 # 890 # 890 # 890 # 891 # 892 # 892 # 892 # 895 # 895 # 895 # 896 # 896 # 896 # 896 # 896 # 897 # 898 # 898 # 898 # 899 # 900 # 900 # 901' # expected: '' not ok 5 - vg inject works perfectly for the position of alignment # got: '1 # 1 # 1 # 3 # 3 # 4 # 4 # 4 # 5 # 7 # 7 # 8 # 8 # 8 # 9 # 11 # 11 # 12 # 12 # 12 # 17 # 17 # 17 # 17 # 17 # 20 # 20 # 20 # 21 # 21 # 25 # 25 # 25 # 31 # 31 # 32 # 33 # 35 # 37 # 40 # 41 # 42 # 45 # 45 # 46 # 48 # 48 # 48 # 48 # 49 # 49 # 50 # 51 # 52 # 52 # 53 # 53 # 53 # 53 # 55 # 56 # 56 # 58 # 58 # 59 # 60 # 60 # 62 # 62 # 64 # 64 # 65 # 66 # 68 # 69 # 69 # 70 # 70 # 70 # 70 # 70 # 71 # 72 # 74 # 75 # 77 # 77 # 77 # 78 # 78 # 78 # 81 # 82 # 83 # 84 # 85 # 86 # 87 # 87 # 87 # 88 # 88 # 88 # 89 # 90 # 90 # 93 # 93 # 94 # 96 # 96 # 97 # 99 # 99 # 100 # 101 # 101 # 102 # 102 # 102 # 102 # 103 # 103 # 104 # 105 # 105 # 106 # 106 # 106 # 107 # 108 # 113 # 113 # 115 # 116 # 116 # 119 # 119 # 120 # 120 # 122 # 123 # 124 # 125 # 125 # 126 # 126 # 127 # 127 # 127 # 128 # 128 # 129 # 130 # 130 # 131 # 131 # 131 # 132 # 134 # 134 # 135 # 136 # 136 # 137 # 137 # 137 # 139 # 140 # 141 # 142 # 142 # 142 # 143 # 143 # 144 # 144 # 145 # 145 # 146 # 147 # 147 # 149 # 150 # 153 # 153 # 154 # 154 # 155 # 156 # 156 # 156 # 157 # 158 # 158 # 158 # 158 # 164 # 164 # 164 # 164 # 165 # 166 # 167 # 167 # 167 # 167 # 168 # 168 # 169 # 170 # 171 # 172 # 172 # 173 # 174 # 175 # 175 # 175 # 177 # 177 # 177 # 178 # 178 # 178 # 178 # 180 # 182 # 183 # 183 # 184 # 184 # 186 # 187 # 188 # 189 # 191 # 193 # 194 # 195 # 197 # 197 # 197 # 197 # 198 # 200 # 200 # 201 # 204 # 205 # 205 # 206 # 207 # 208 # 209 # 210 # 213 # 214 # 214 # 215 # 215 # 216 # 217 # 218 # 218 # 219 # 219 # 219 # 221 # 224 # 224 # 224 # 229 # 229 # 232 # 232 # 232 # 233 # 234 # 234 # 234 # 234 # 237 # 237 # 237 # 238 # 239 # 240 # 240 # 243 # 244 # 245 # 246 # 247 # 250 # 251 # 253 # 253 # 255 # 258 # 258 # 260 # 262 # 265 # 266 # 267 # 268 # 268 # 270 # 270 # 270 # 272 # 273 # 273 # 274 # 274 # 274 # 275 # 276 # 276 # 277 # 277 # 280 # 282 # 283 # 284 # 285 # 285 # 286 # 287 # 287 # 288 # 288 # 289 # 290 # 290 # 291 # 291 # 291 # 291 # 293 # 294 # 294 # 297 # 297 # 298 # 298 # 298 # 300 # 300 # 304 # 306 # 306 # 306 # 307 # 308 # 308 # 308 # 309 # 309 # 310 # 311 # 311 # 312 # 312 # 312 # 313 # 313 # 313 # 314 # 314 # 314 # 315 # 316 # 317 # 319 # 320 # 322 # 323 # 323 # 325 # 325 # 326 # 327 # 332 # 334 # 334 # 334 # 334 # 335 # 336 # 336 # 339 # 339 # 340 # 343 # 344 # 344 # 344 # 345 # 345 # 347 # 347 # 350 # 350 # 351 # 353 # 357 # 357 # 357 # 358 # 358 # 359 # 363 # 363 # 364 # 365 # 365 # 366 # 366 # 367 # 370 # 372 # 373 # 373 # 373 # 375 # 375 # 377 # 379 # 379 # 380 # 380 # 381 # 383 # 385 # 386 # 387 # 389 # 390 # 390 # 391 # 394 # 396 # 399 # 399 # 400 # 400 # 401 # 403 # 403 # 404 # 404 # 404 # 405 # 406 # 406 # 407 # 407 # 408 # 411 # 412 # 412 # 414 # 414 # 415 # 415 # 417 # 418 # 421 # 423 # 425 # 425 # 425 # 425 # 425 # 425 # 425 # 426 # 426 # 427 # 427 # 427 # 428 # 429 # 429 # 430 # 430 # 430 # 430 # 431 # 432 # 433 # 434 # 434 # 435 # 436 # 439 # 440 # 441 # 442 # 443 # 447 # 447 # 448 # 449 # 449 # 450 # 451 # 451 # 452 # 453 # 453 # 453 # 454 # 455 # 455 # 456 # 457 # 458 # 458 # 460 # 460 # 460 # 460 # 462 # 462 # 464 # 464 # 465 # 465 # 466 # 466 # 466 # 467 # 468 # 470 # 471 # 471 # 471 # 471 # 471 # 472 # 473 # 473 # 473 # 474 # 477 # 477 # 478 # 478 # 478 # 480 # 480 # 481 # 482 # 483 # 483 # 483 # 484 # 484 # 484 # 487 # 488 # 490 # 491 # 492 # 493 # 493 # 493 # 494 # 494 # 495 # 497 # 500 # 500 # 501 # 501 # 502 # 503 # 504 # 505 # 506 # 506 # 508 # 508 # 510 # 511 # 514 # 515 # 516 # 516 # 518 # 520 # 521 # 522 # 522 # 523 # 523 # 525 # 525 # 525 # 526 # 527 # 527 # 528 # 530 # 530 # 531 # 532 # 533 # 535 # 537 # 537 # 537 # 538 # 539 # 542 # 544 # 545 # 546 # 546 # 547 # 549 # 549 # 551 # 551 # 552 # 552 # 552 # 553 # 554 # 554 # 556 # 557 # 558 # 558 # 560 # 561 # 563 # 565 # 565 # 566 # 567 # 567 # 569 # 569 # 569 # 570 # 571 # 572 # 572 # 572 # 572 # 573 # 575 # 577 # 578 # 579 # 581 # 582 # 584 # 584 # 585 # 585 # 588 # 589 # 590 # 593 # 593 # 595 # 596 # 597 # 598 # 599 # 600 # 600 # 600 # 600 # 601 # 601 # 602 # 602 # 603 # 604 # 605 # 605 # 606 # 608 # 608 # 608 # 609 # 611 # 612 # 612 # 613 # 613 # 614 # 614 # 615 # 615 # 615 # 616 # 618 # 618 # 619 # 619 # 620 # 620 # 620 # 622 # 625 # 625 # 626 # 626 # 627 # 628 # 629 # 629 # 630 # 630 # 630 # 631 # 632 # 632 # 634 # 634 # 634 # 636 # 636 # 636 # 637 # 637 # 639 # 639 # 639 # 641 # 642 # 642 # 644 # 644 # 645 # 649 # 650 # 650 # 651 # 654 # 655 # 656 # 656 # 657 # 658 # 660 # 661 # 661 # 663 # 667 # 668 # 668 # 671 # 672 # 674 # 674 # 674 # 675 # 676 # 676 # 676 # 676 # 677 # 677 # 680 # 681 # 683 # 684 # 684 # 687 # 688 # 690 # 692 # 693 # 693 # 693 # 696 # 697 # 697 # 700 # 700 # 701 # 702 # 702 # 702 # 703 # 703 # 704 # 704 # 704 # 704 # 705 # 706 # 706 # 707 # 707 # 711 # 713 # 713 # 714 # 718 # 720 # 722 # 723 # 724 # 724 # 724 # 725 # 726 # 726 # 726 # 728 # 729 # 729 # 730 # 733 # 734 # 734 # 735 # 738 # 738 # 738 # 741 # 743 # 746 # 747 # 749 # 751 # 752 # 752 # 753 # 754 # 755 # 756 # 758 # 758 # 759 # 759 # 760 # 761 # 761 # 762 # 763 # 763 # 764 # 765 # 767 # 767 # 768 # 769 # 770 # 770 # 770 # 771 # 771 # 771 # 775 # 776 # 776 # 777 # 779 # 779 # 779 # 779 # 781 # 781 # 782 # 785 # 787 # 787 # 787 # 788 # 789 # 789 # 790 # 790 # 791 # 791 # 792 # 792 # 792 # 793 # 793 # 793 # 794 # 796 # 796 # 802 # 806 # 806 # 807 # 808 # 809 # 809 # 809 # 810 # 810 # 812 # 813 # 818 # 825 # 825 # 826 # 826 # 827 # 827 # 828 # 829 # 830 # 830 # 834 # 834 # 835 # 835 # 836 # 837 # 841 # 844 # 845 # 845 # 845 # 845 # 846 # 846 # 850 # 850 # 852 # 853 # 853 # 854 # 855 # 856 # 858 # 859 # 860 # 861 # 862 # 862 # 863 # 864 # 866 # 869 # 870 # 870 # 871 # 873 # 874 # 874 # 876 # 877 # 877 # 877 # 877 # 879 # 881 # 882 # 883 # 884 # 885 # 885 # 885 # 886 # 887 # 888 # 889 # 889 # 889 # 889 # 889 # 890 # 890 # 890 # 890 # 891 # 892 # 892 # 892 # 895 # 895 # 895 # 896 # 896 # 896 # 896 # 896 # 897 # 898 # 898 # 898 # 899 # 900 # 900 # 901' # expected: '' not ok 6 - vg inject works perfectly for the mapping quality of alignment # got: '1000' # expected: '0' not ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph # got: '100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 19M1D81M # 24M1I75M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 62M1D32M1D6M # 100M # 100M # 60M1I39M # 100M # 100M # 60M1D40M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 52M1D42M1I5M # 14M1D86M # 19M1I80M # 100M # 100M # 100M # 79M1D21M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 56M1D22M1I21M # 100M # 100M # 100M # 29M1I70M # 100M # 34M1I65M # 16M1D84M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 75M1I24M # 100M # 100M # 73M1D27M # 100M # 100M # 52M1D48M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 21M1I78M # 100M # 100M # 3M1D97M # 100M # 100M # 8M1D92M # 100M # 67M1I32M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 78M1D22M # 100M # 100M # 100M # 100M # 15M1D85M # 94M1I5M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 10M1I89M # 100M # 100M # 100M # 100M # 100M # 22M1I77M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 26M1D74M # 100M # 100M # 100M # 100M # 100M # 100M # 12M1I64M1D23M # 100M # 100M # 100M # 28M1I71M # 5M1I94M # 100M # 100M # 100M # 100M # 3M1D97M # 83M1D10M1I6M # 80M1D20M # 100M # 100M # 100M # 100M # 100M # 79M1D10M1I10M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 39M1I60M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 3M1D64M1I32M # 59M1I40M # 100M # 100M # 100M # 100M # 60M1I39M # 63M1I36M # 100M # 29M1D43M1D28M # 100M # 100M # 100M # 33M1D67M # 100M # 100M # 100M # 100M # 55M1I44M # 100M # 100M # 100M # 46M1D54M # 100M # 100M # 100M # 100M # 8M1I91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 100M # 100M # 100M # 100M # 100M # 100M # 36M1D64M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 86M1D14M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 67M1I32M # 100M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 17M1D26M1D57M # 100M # 100M # 100M # 100M # 100M # 4M1I95M # 100M # 100M # 100M # 35M1I64M # 100M # 13M1I86M # 100M # 46M1D54M # 44M1I55M # 74M1I25M # 100M # 100M # 100M # 8M1D19M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D43M # 14M1D86M # 100M # 100M # 28M1I71M # 100M # 100M # 100M # 31M1I68M # 100M # 100M # 100M # 86M1D14M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 91M1I8M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 35M1I64M # 100M # 100M # 100M # 56M1D44M # 100M # 13M1D45M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 100M # 100M # 15M1D85M # 100M # 100M # 100M # 42M1D58M # 100M # 100M # 100M # 100M # 100M # 100M # 41M1I58M # 100M # 100M # 100M # 100M # 24M1D76M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 48M1D52M # 68M1D32M # 39M1D51M1D10M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 100M # 100M # 100M # 50M1I49M # 100M # 100M # 100M # 63M1I17M1I18M # 5M1D95M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 40M1I59M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 72M1I27M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 100M # 93M1D7M # 100M # 100M # 43M1I9M1I46M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 82M1D18M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 49M1I50M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 23M1I76M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1I6M1I24M # 100M # 100M # 100M # 100M # 100M # 100M # 45M1D55M # 100M # 43M1I39M1I16M # 100M # 93M1D7M # 66M1I33M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 59M1D41M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1D34M # 94M1D6M # 100M # 100M # 100M # 46M1I53M # 100M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D13M1D18M1D12M # 84M1D16M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1D14M # 100M # 100M # 100M # 95M5S # 100M # 100M # 100M # 100M # 22M1D78M # 100M # 100M # 100M # 2S98M # 100M # 100M # 95M1I4M # 100M # 95M1D5M # 100M # 76M1D24M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 5M1D69M1D26M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 65M1I34M # 100M # 100M # 100M # 100M # 100M # 18M1D82M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1I62M # 100M # 100M # 100M # 67M1I32M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 28M1I71M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 4M1D96M # 69M1I30M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 16M1I32M1D51M # 100M # 100M # 100M # 84M1I15M # 100M # 100M # 12M1D88M # 100M # 35M1I64M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 14M1D86M # 68M1D32M # 27M1D73M # 100M # 100M # 71M1I28M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M # 100M # 35M1D65M # 100M # 4M1I61M1I33M # 100M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1I33M # 100M # 50M1I49M # 100M # 100M # 100M # 100M # 100M # 38M1I52M1I8M # 100M # 100M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 27M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1D63M # 100M # 100M # 43M1D18M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 88M1D12M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 8M1D24M1I67M # 88M1D12M # 100M # 100M # 100M # 50M1I49M # 44M1D56M # 100M # 56M1D44M # 100M # 34M1I65M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 42M1D58M # 35M1I64M # 100M # 100M # 100M # 100M # 24M1D76M # 76M1I23M # 100M # 100M # 68M1I31M # 100M # 100M # 6M1I93M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 34M1D66M # 31M1D69M # 100M # 100M # 100M # 100M # 100M # 100M # 15M1I84M # 100M # 100M # 100M # 5M1I94M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 64M1D36M # 100M # 96M1D4M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 25M1D75M # 85M1I14M # 48M1D52M # 100M # 100M # 21M1D79M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M' # expected: '' not ok 8 - vg inject works perfectly for the cigar of alignment # got: '100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 19M1D81M # 24M1I75M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 62M1D32M1D6M # 100M # 100M # 60M1I39M # 100M # 100M # 60M1D40M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 52M1D42M1I5M # 14M1D86M # 19M1I80M # 100M # 100M # 100M # 79M1D21M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 56M1D22M1I21M # 100M # 100M # 100M # 29M1I70M # 100M # 34M1I65M # 16M1D84M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 75M1I24M # 100M # 100M # 73M1D27M # 100M # 100M # 52M1D48M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 21M1I78M # 100M # 100M # 3M1D97M # 100M # 100M # 8M1D92M # 100M # 67M1I32M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 78M1D22M # 100M # 100M # 100M # 100M # 15M1D85M # 94M1I5M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 10M1I89M # 100M # 100M # 100M # 100M # 100M # 22M1I77M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 26M1D74M # 100M # 100M # 100M # 100M # 100M # 100M # 12M1I64M1D23M # 100M # 100M # 100M # 28M1I71M # 5M1I94M # 100M # 100M # 100M # 100M # 3M1D97M # 83M1D10M1I6M # 80M1D20M # 100M # 100M # 100M # 100M # 100M # 79M1D10M1I10M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 39M1I60M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 3M1D64M1I32M # 59M1I40M # 100M # 100M # 100M # 100M # 60M1I39M # 63M1I36M # 100M # 29M1D43M1D28M # 100M # 100M # 100M # 33M1D67M # 100M # 100M # 100M # 100M # 55M1I44M # 100M # 100M # 100M # 46M1D54M # 100M # 100M # 100M # 100M # 8M1I91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 100M # 100M # 100M # 100M # 100M # 100M # 36M1D64M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 86M1D14M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 67M1I32M # 100M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 17M1D26M1D57M # 100M # 100M # 100M # 100M # 100M # 4M1I95M # 100M # 100M # 100M # 35M1I64M # 100M # 13M1I86M # 100M # 46M1D54M # 44M1I55M # 74M1I25M # 100M # 100M # 100M # 8M1D19M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D43M # 14M1D86M # 100M # 100M # 28M1I71M # 100M # 100M # 100M # 31M1I68M # 100M # 100M # 100M # 86M1D14M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 91M1I8M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 35M1I64M # 100M # 100M # 100M # 56M1D44M # 100M # 13M1D45M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 100M # 100M # 15M1D85M # 100M # 100M # 100M # 42M1D58M # 100M # 100M # 100M # 100M # 100M # 100M # 41M1I58M # 100M # 100M # 100M # 100M # 24M1D76M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 48M1D52M # 68M1D32M # 39M1D51M1D10M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 100M # 100M # 100M # 50M1I49M # 100M # 100M # 100M # 63M1I17M1I18M # 5M1D95M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 40M1I59M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 72M1I27M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 100M # 93M1D7M # 100M # 100M # 43M1I9M1I46M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 82M1D18M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 49M1I50M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 23M1I76M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1I6M1I24M # 100M # 100M # 100M # 100M # 100M # 100M # 45M1D55M # 100M # 43M1I39M1I16M # 100M # 93M1D7M # 66M1I33M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 59M1D41M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1D34M # 94M1D6M # 100M # 100M # 100M # 46M1I53M # 100M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D13M1D18M1D12M # 84M1D16M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1D14M # 100M # 100M # 100M # 95M5S # 100M # 100M # 100M # 100M # 22M1D78M # 100M # 100M # 100M # 2S98M # 100M # 100M # 95M1I4M # 100M # 95M1D5M # 100M # 76M1D24M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 5M1D69M1D26M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 65M1I34M # 100M # 100M # 100M # 100M # 100M # 18M1D82M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1I62M # 100M # 100M # 100M # 67M1I32M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 28M1I71M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 4M1D96M # 69M1I30M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 16M1I32M1D51M # 100M # 100M # 100M # 84M1I15M # 100M # 100M # 12M1D88M # 100M # 35M1I64M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 14M1D86M # 68M1D32M # 27M1D73M # 100M # 100M # 71M1I28M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M # 100M # 35M1D65M # 100M # 4M1I61M1I33M # 100M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1I33M # 100M # 50M1I49M # 100M # 100M # 100M # 100M # 100M # 38M1I52M1I8M # 100M # 100M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 27M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1D63M # 100M # 100M # 43M1D18M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 88M1D12M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 8M1D24M1I67M # 88M1D12M # 100M # 100M # 100M # 50M1I49M # 44M1D56M # 100M # 56M1D44M # 100M # 34M1I65M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 42M1D58M # 35M1I64M # 100M # 100M # 100M # 100M # 24M1D76M # 76M1I23M # 100M # 100M # 68M1I31M # 100M # 100M # 6M1I93M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 34M1D66M # 31M1D69M # 100M # 100M # 100M # 100M # 100M # 100M # 15M1I84M # 100M # 100M # 100M # 5M1I94M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 64M1D36M # 100M # 96M1D4M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 25M1D75M # 85M1I14M # 48M1D52M # 100M # 100M # 21M1D79M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M' # expected: '' not ok 9 - vg inject preserves all reads # got: '0' # expected: '470' ok 10 - vg inject works perfectly for the reads flagged as is_reverse Failed 9/10 subtests t/40_vg_gamcompare.t: line 11: 1198649 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > s.vg t/40_vg_gamcompare.t: line 12: 1198650 Illegal instruction (core dumped) vg index -x s.xg -g s.gcsa s.vg t/40_vg_gamcompare.t: line 13: 1198651 Illegal instruction (core dumped) vg sim -n 1000 -l 100 -e 0.01 -i 0.005 -x s.xg -a > s.sim t/40_vg_gamcompare.t: line 20: 1198663 Illegal instruction (core dumped) vg map -x s.xg -g s.gcsa -s "AATCTCTCTGAACTTCAGTTTAATTATC" > read1.gam t/40_vg_gamcompare.t: line 21: 1198664 Illegal instruction (core dumped) vg annotate -a read1.gam -p -x s.xg > read1.single.gam t/40_vg_gamcompare.t: line 22: 1198665 Illegal instruction (core dumped) vg annotate -a read1.gam -m -x s.xg > read1.multi.gam t/40_vg_gamcompare.t: line 23: 1198666 Illegal instruction (core dumped) vg map -x s.xg -g s.gcsa -s "TCTAATATGGAGATGATACTACTGACAG" > read2.gam t/40_vg_gamcompare.t: line 24: 1198667 Illegal instruction (core dumped) vg annotate -a read2.gam -p -x s.xg > read2.single.gam t/40_vg_gamcompare.t: line 25: 1198668 Illegal instruction (core dumped) vg annotate -a read2.gam -m -x s.xg > read2.multi.gam t/40_vg_gamcompare.t .. 1..5 not ok 1 - gamcompare completes # got: '0' # expected: '1000' not ok 2 - gamcompare says the truth is correctly mapped # got: '0' # expected: '1000' not ok 3 - Reads annotated with leftmost position only are close enough at a long distance # got: '0' # expected: '1' ok 4 - Reads annotated with leftmost position only are too far apart at a short distance not ok 5 - Reads annotated with multiple positions only are close enough at a short distance # got: '0' # expected: '1' Failed 4/5 subtests t/41_vg_viz.t: line 11: 1198687 Illegal instruction (core dumped) vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg t/41_vg_viz.t: line 12: 1198688 Illegal instruction (core dumped) vg index -x t.xg -g t.gcsa t.vg t/41_vg_viz.t: line 13: 1198692 Illegal instruction (core dumped) vg sim -l 30 -n 100 -x t.xg -a t/41_vg_viz.t: line 13: 1198689 Illegal instruction vg map -G <(vg sim -l 30 -n 100 -x t.xg -a) -d t 1198690 Illegal instruction (core dumped) | vg pack -x t.xg -o t.cx -g - t/41_vg_viz.t: line 15: 1198693 Illegal instruction (core dumped) vg viz -x t.xg -o t.svg -i t.cx -n alignments t/41_vg_viz.t ......... 1..1 ok 1 - vg viz runs ok t/42_vg_gamsort.t: line 11: 1198702 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/42_vg_gamsort.t: line 12: 1198703 Illegal instruction (core dumped) vg index -x x.xg x.vg t/42_vg_gamsort.t: line 13: 1198704 Illegal instruction (core dumped) vg sim -n 1000 -l 100 -e 0.01 -i 0.005 -x x.xg -a > x.gam t/42_vg_gamsort.t: line 15: 1198705 Illegal instruction (core dumped) vg gamsort x.gam > x.sorted.gam t/42_vg_gamsort.t: line 22: 1198715 Illegal instruction (core dumped) vg gamsort x.gam -i x.sorted.gam.gai > x.sorted.gam t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID not ok 2 - sorted GAMs can be indexed during the sort # got: '132' # expected: '0' Failed 1/2 subtests t/43_vg_simplify.t: line 10: 1198718 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg t/43_vg_simplify.t: line 13: 1198719 Illegal instruction (core dumped) vg simplify --algorithm small x.vg > x.small.vg 2> /dev/null t/43_vg_simplify.t: line 18: 1198724 Illegal instruction (core dumped) vg simplify --algorithm rare --min-count 2 -v small/x.vcf.gz x.vg > x.rare.vg t/43_vg_simplify.t: line 21: 1198725 Illegal instruction (core dumped) vg validate x.rare.vg t/43_vg_simplify.t .... 1..5 not ok 1 - vg simplify runs through when popping small bubbles # got: '132' # expected: '0' not ok 2 - simplification pops all the bubbles in a simple graph # got: '' # expected: '1' not ok 3 - vg simplify runs through when removing rare variants # got: '132' # expected: '0' not ok 4 - the graph is valid after removing rare variants # got: '132' # expected: '0' not ok 5 - simplification keeps only some variants # got: '' # expected: '118' Failed 5/5 subtests t/44_vg_benchmark.t: line 10: 1198732 Illegal instruction (core dumped) vg benchmark > /dev/null t/44_vg_benchmark.t ... 1..1 not ok 1 - vg benchmark completes succesfully # got: '132' # expected: '0' Failed 1/1 subtests t/45_vg_sort.t: line 12: 1198734 Illegal instruction (core dumped) vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 1198735 (core dumped) | vg mod -X 1 - > giab.vg t/45_vg_sort.t: line 21: 1198740 Illegal instruction (core dumped) vg sort -a id -I giab.sorted.vg.vgi giab.vg > giab.sorted.vg t/45_vg_sort.t: line 25: 1198741 Illegal instruction (core dumped) vg sort -a topo giab.vg > /dev/null t/45_vg_sort.t: line 28: 1198742 Illegal instruction (core dumped) vg sort -a eades -r q giab.vg > /dev/null t/45_vg_sort.t: line 31: 1198743 Illegal instruction (core dumped) vg sort -a max-flow -r q giab.vg > /dev/null t/45_vg_sort.t ........ 1..5 not ok 1 - ids in our test graph are not initially in sorted order # got: '0' # expected: '1' not ok 2 - a vg graph can be sorted and indexed by ID without crashing # got: '132' # expected: '0' not ok 3 - a vg graph can be sorted topologically # got: '132' # expected: '0' not ok 4 - a vg graph can be sorted with Eades algorithm without crashing # got: '132' # expected: '0' not ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing # got: '132' # expected: '0' Failed 5/5 subtests t/46_vg_minimizer.t: line 12: 1198746 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/46_vg_minimizer.t: line 13: 1198747 Illegal instruction (core dumped) vg index -x x.xg -G x.gbwt -v small/xy2.vcf.gz x.vg t/46_vg_minimizer.t: line 14: 1198748 Illegal instruction (core dumped) vg snarls -T x.vg > x.snarls t/46_vg_minimizer.t: line 15: 1198749 Illegal instruction (core dumped) vg index -s x.snarls -j x.dist -x x.xg t/46_vg_minimizer.t: line 18: 1198750 Illegal instruction (core dumped) vg minimizer -i x.mi -g x.gbwt x.xg t/46_vg_minimizer.t: line 22: 1198751 Illegal instruction (core dumped) vg minimizer -t 1 -i x.mi -g x.gbwt x.xg t/46_vg_minimizer.t: line 24: 1198752 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex x.mi > x.extracted.mi t/46_vg_minimizer.t: line 28: 1198756 Illegal instruction (core dumped) vg minimizer -t 1 -i x.mi -b -g x.gbwt x.xg t/46_vg_minimizer.t: line 30: 1198757 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex x.mi > x.extracted.mi t/46_vg_minimizer.t: line 34: 1198761 Illegal instruction (core dumped) vg minimizer -t 1 -k 7 -w 3 -i x.mi -g x.gbwt x.xg t/46_vg_minimizer.t: line 36: 1198762 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex x.mi > x.extracted.mi t/46_vg_minimizer.t: line 40: 1198766 Illegal instruction (core dumped) vg gbwt -x x.xg -g x.gg x.gbwt t/46_vg_minimizer.t: line 41: 1198767 Illegal instruction (core dumped) vg minimizer -t 1 -g x.gbwt -G -i x.mi x.gg t/46_vg_minimizer.t: line 43: 1198768 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex x.mi > x.extracted.mi t/46_vg_minimizer.t: line 47: 1198772 Illegal instruction (core dumped) vg minimizer -t 1 -i x.mi -g x.gbwt -d x.dist -G x.gg t/46_vg_minimizer.t: line 49: 1198773 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex x.mi > x.extracted.mi t/46_vg_minimizer.t: line 56: 1198778 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null t/46_vg_minimizer.t: line 57: 1198779 Illegal instruction (core dumped) vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null t/46_vg_minimizer.t: line 58: 1198780 Illegal instruction (core dumped) vg ids -j x.vg y.vg t/46_vg_minimizer.t: line 59: 1198781 Illegal instruction (core dumped) vg index -x x.xg -G x.gbwt -v small/xy2.vcf.gz x.vg t/46_vg_minimizer.t: line 60: 1198782 Illegal instruction (core dumped) vg index -x y.xg -G y.gbwt -v small/xy2.vcf.gz y.vg t/46_vg_minimizer.t: line 63: 1198783 Illegal instruction (core dumped) vg minimizer -t 1 -i x.mi -g x.gbwt x.xg t/46_vg_minimizer.t: line 65: 1198784 Illegal instruction (core dumped) vg minimizer -t 1 -l x.mi -i xy.mi -g y.gbwt y.xg t/46_vg_minimizer.t: line 67: 1198785 Illegal instruction (core dumped) vg view --extract-tag MinimizerIndex xy.mi > xy.extracted.mi t/46_vg_minimizer.t ... 1..14 not ok 1 - default parameters # got: '132' # expected: '0' not ok 2 - single-threaded construction # got: '132' # expected: '0' not ok 3 - construction is deterministic # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '58b2bd98902df9acbe416bcfde649571' not ok 4 - syncmer index # got: '132' # expected: '0' not ok 5 - construction is deterministic # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '111bb0658db34d88a3a075f269513a36' not ok 6 - minimizer parameters # got: '132' # expected: '0' not ok 7 - setting -k -w works correctly # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'c69f4f2dfab192fc66055dcf2fa8a7da' not ok 8 - construction from GBWTGraph # got: '132' # expected: '0' not ok 9 - construction is deterministic # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '58b2bd98902df9acbe416bcfde649571' not ok 10 - construction with payload # got: '132' # expected: '0' not ok 11 - construction is deterministic # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '58a6780c18921e4f6701b57fdb9c2e44' not ok 12 - multiple graphs: first # got: '132' # expected: '0' not ok 13 - multiple graphs: second # got: '132' # expected: '0' not ok 14 - construction is deterministic # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '7500d106741f2dd8aa34aa178c917832' Failed 14/14 subtests t/47_vg_dotplot.t: line 10: 1198794 Illegal instruction (core dumped) vg msga -f GRCh38_alts/FASTA/HLA/V-352962.fa -t 1 -k 16 > hla.vg t/47_vg_dotplot.t: line 11: 1198795 Illegal instruction (core dumped) vg index -x hla.xg hla.vg t/47_vg_dotplot.t: line 12: 1198796 Illegal instruction (core dumped) vg dotplot -x hla.xg > /dev/null t/47_vg_dotplot.t ..... 1..1 not ok 1 - vg dotplot runs successfully # got: '132' # expected: '0' Failed 1/1 subtests t/48_vg_convert.t: line 10: 1198799 Illegal instruction (core dumped) vg construct -r complex/c.fa -v complex/c.vcf.gz > c.vg t/48_vg_convert.t: line 11: 1198809 Illegal instruction (core dumped) vg paths -v c.vg -E t/48_vg_convert.t: line 13: 1198812 Illegal instruction (core dumped) vg convert c.vg -x > c.xg t/48_vg_convert.t: line 14: 1198813 Illegal instruction (core dumped) vg convert c.xg -v > c1.vg t/48_vg_convert.t: line 15: 1198823 Illegal instruction (core dumped) vg paths -v c1.vg -E t/48_vg_convert.t: line 21: 1198828 Illegal instruction (core dumped) vg convert c.vg -a > c.hg t/48_vg_convert.t: line 22: 1198829 Illegal instruction (core dumped) vg convert c.hg -v > c1.vg t/48_vg_convert.t: line 23: 1198840 Illegal instruction (core dumped) vg paths -v c1.vg -E t/48_vg_convert.t: line 29: 1198844 Illegal instruction (core dumped) vg convert c.vg -p > c.pg t/48_vg_convert.t: line 30: 1198845 Illegal instruction (core dumped) vg convert c.pg -v > c1.vg t/48_vg_convert.t: line 31: 1198855 Illegal instruction (core dumped) vg paths -v c1.vg -E t/48_vg_convert.t: line 37: 1198860 Illegal instruction (core dumped) vg convert c.vg -o > c.odgi t/48_vg_convert.t: line 38: 1198861 Illegal instruction (core dumped) vg convert c.odgi -v > c1.vg t/48_vg_convert.t: line 39: 1198873 Illegal instruction (core dumped) vg paths -v c1.vg -E t/48_vg_convert.t: line 46: 1198876 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/48_vg_convert.t: line 47: 1198877 Illegal instruction (core dumped) vg view x.vg > x.gfa t/48_vg_convert.t: line 62: 1198931 Illegal instruction (core dumped) vg construct -r small/x.fa -v small/x.vcf.gz > x.vg t/48_vg_convert.t: line 63: 1198932 Illegal instruction (core dumped) vg index x.vg -g x.gcsa t/48_vg_convert.t: line 64: 1198933 Illegal instruction (core dumped) vg sim -x x.vg -n 10 -s 23 -a > sim.gam t/48_vg_convert.t: line 65: 1198934 Illegal instruction (core dumped) vg map -x x.vg -g x.gcsa -G sim.gam > sim-rm.gam t/48_vg_convert.t: line 66: 1198935 Illegal instruction (core dumped) vg convert x.vg -G sim-rm.gam -t 1 > sim-rm.gaf t/48_vg_convert.t: line 67: 1198936 Illegal instruction (core dumped) vg convert x.vg -F sim-rm.gaf -t 1 1198937 (core dumped) | vg convert x.vg -G - -t 1 > sim-rm2.gaf t/48_vg_convert.t: line 81: 1198951 Illegal instruction (core dumped) vg map -s "TAATGGATATGTTAAGCTTTTTTTTTCTTTGATTTATTTGAAAAGACGTTTGACAATCTATCGGGTAATGTGGGGAAA" -x x.vg -g x.gcsa > mut.gam t/48_vg_convert.t: line 83: 1198952 Illegal instruction (core dumped) vg map -s "TTTCCCCACATTACCCGATAGATTGTCAAACGTCTTTTCAAATAAATCAAAGAAAAAAAAAGCTTAACATATCCATTA" -x x.vg -g x.gcsa >> mut.gam t/48_vg_convert.t: line 85: 1198953 Illegal instruction (core dumped) vg convert x.vg -G mut.gam -t 1 > mut.gaf t/48_vg_convert.t: line 86: 1198954 Illegal instruction (core dumped) vg convert x.vg -F mut.gaf -t 1 > mut-back.gam t/48_vg_convert.t: line 97: 1198965 Illegal instruction (core dumped) vg convert x.vg -G mut-back.gam -t 1 > mut-back.gaf t/48_vg_convert.t: line 103: 1198968 Illegal instruction (core dumped) vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg 2> /dev/null t/48_vg_convert.t: line 104: 1198969 Illegal instruction (core dumped) vg sim -n 10000 -s 23 -a -x z.vg > sim.gam t/48_vg_convert.t: line 105: 1198970 Illegal instruction (core dumped) vg construct -r 1mb1kgp/z.fa > zflat.vg t/48_vg_convert.t: line 106: 1198971 Illegal instruction (core dumped) vg index zflat.vg -g zflat.gcsa t/48_vg_convert.t: line 107: 1198972 Illegal instruction (core dumped) vg map -x zflat.vg -g zflat.gcsa -G sim.gam > sim-map.gam t/48_vg_convert.t: line 109: 1198975 Illegal instruction (core dumped) vg convert zflat.vg -F sim-map.gaf.gz > sim-map-back.gam t/48_vg_convert.t: line 120: 1198988 Done printf '{"name": "split", "path": {"mapping": [{"edit": [{"from_length": 13, "to_length": 13}], "position": {"node_id": "1", "offset": "10"}}, {"edit": [{"from_length": 2, "to_length": 2}], "position": {"node_id": "3", "offset": "5"}}]}}' 1198989 Illegal instruction (core dumped) | vg view -JaG - > split.gam t/48_vg_convert.t: line 121: 1198990 Illegal instruction (core dumped) vg convert zflat.vg -G split.gam > split.gaf t/48_vg_convert.t: line 123: 1198992 Illegal instruction (core dumped) vg convert zflat.vg -F split.gaf 1198993 (core dumped) | vg convert zflat.vg -G - > split-back.gaf t/48_vg_convert.t: line 141: 1198996 Done printf "H\tVN:Z:1.0 S\t73333\tGGTGGGCGAGGACCTCCACACGTGTCACCA S\t73368\tGCCCCT S\t72943\tGGCGACTCTTCAGCAAGCCCCTCCACACGTGT S\t72940\tC S\t72941\tGGCCAGGT S\t73255\tACTCTTCAGCAGGCCCCTCTGGT S\t72942\tGGGCGAGGACCTCCACACGTGTCACCAGGCCA S\t73318\tTCAGCA S\t73367\tA S\t73271\tA S\t73289\tC S\t73317\tC\n" 1198997 Illegal instruction (core dumped) | vg convert -g - -p > soft.pg t/48_vg_convert.t: line 142: 1198998 Done printf '{"annotation": {"fragment_length": 242, "fragment_length_distribution": "-I 561.110526 -D 141.152986", "mapq_applied_cap": 23.832780374978935, "mapq_extended_cap": 15, "mapq_uncapped": 10.325140756048304, "secondary_scores": [187.15265582416521, 182.4063994408188]}, "identity": 0.89682539682539686, "mapping_quality": 10, "name": "ERR903030.2067", "path": {"mapping": [{"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "72943", "offset": "26"}}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"is_reverse": true, "node_id": "72942"}, "rank": "1"}, {"edit": [{"from_length": 23, "to_length": 23}], "position": {"is_reverse": true, "node_id": "73255"}, "rank": "2"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73271"}, "rank": "3"}, {"edit": [{"from_length": 8, "to_length": 8}], "position": {"is_reverse": true, "node_id": "72941"}, "rank": "4"}, {"edit": [{"from_length": 7, "to_length": 7}, {"from_length": 1, "sequence": "C", "to_length": 1}, {"from_length": 2, "to_length": 2}, {"from_length": 1, "sequence": "G", "to_length": 1}, {"from_length": 19, "to_length": 19}], "position": {"is_reverse": true, "node_id": "73333"}, "rank": "5"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "72940"}, "rank": "6"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73289"}, "rank": "7"}, {"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "73368"}, "rank": "8"}, {"edit": [{"from_length": 1, "sequence": "G", "to_length": 1}], "position": {"is_reverse": true, "node_id": "73367"}, "rank": "9"}, {"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "73318"}, "rank": "10"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73317"}, "rank": "11"}, {"edit": [{"sequence": "GGGTGGCCTG", "to_length": 10}], "position": {"is_reverse": true, "node_id": "73317", "offset": "1"}, "rank": "12"}]}, "quality": "ISEhISEmJiUmJCYmJSYlJiYmJiYmJCYjJiYdIRsmIyUmJiYmJiElJg4PDx0PDyEkIhsYJCYiECQQJBAcGR0kHx0QGSQPJCImHSElHR0PJA4OGyQbIxwPIg0iHw8PGRwiIR0jAgICAgICAgICAgICAgICAgICAgICAgICAgIC", "sample_name": "HG00514_961a37c_gssw", "score": 106, "sequence": "GTCGCCTGGCCTGGTGACACGTGTGGAGGTCCTCGCCCACCAGAGGGGCCTGCTGAAGAGTTACCTGGCCTGGTGACCCGGGTGGAGGTCCTCGCCCACCGGAGGGGCGTGCTGAGGGGTGGCCTG"}' 1198999 Illegal instruction (core dumped) | vg view -JaG - > soft.gam t/48_vg_convert.t: line 143: 1199000 Illegal instruction (core dumped) vg convert soft.pg -G soft.gam > soft.gaf t/48_vg_convert.t: line 149: 1199007 Illegal instruction (core dumped) vg convert soft.pg -F soft.gaf 1199008 (core dumped) | vg convert soft.pg -G - > soft2.gaf t/48_vg_convert.t: line 156: 1199011 Done printf "H\tVN:Z:1.0 S\t91194329\tAGGAAGGAGAGGGAG\n" 1199012 Illegal instruction (core dumped) | vg convert -g - -p > floating-ins.pg t/48_vg_convert.t: line 157: 1199013 Done printf '{"annotation": {"fragment_length": 1098, "fragment_length_distribution": "-I 542.973684 -D 141.206118", "mapq_applied_cap": 46.364361584299516, "mapq_extended_cap": "Infinity", "mapq_uncapped": 1.5051499783199018, "rescued": true, "secondary_scores": [99.415737573445895]}, "mapping_quality": 1, "name": "ERR903030.51990324", "path": {"mapping": [{"edit": [{"sequence": "GGGCACGGTGGCTCACAGCTGTCACCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", "to_length": 126}], "position": {"is_reverse": true, "node_id": "91194329", "offset": "15"}, "rank": "1"}]}, "quality": "ISEhICEhJCIkJiYdJiUQJSYmHyMmIxAkJiICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIC", "sample_name": "HG00514_961a37c", "sequence": "GGGCACGGTGGCTCACAGCTGTCACCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"}' 1199014 Illegal instruction (core dumped) | vg view -JaG - > floating-ins.gam t/48_vg_convert.t: line 158: 1199015 Illegal instruction (core dumped) vg convert floating-ins.pg -G floating-ins.gam > floating-ins.gaf t/48_vg_convert.t: line 164: 1199022 Illegal instruction (core dumped) vg convert floating-ins.pg -F floating-ins.gaf 1199023 (core dumped) | vg convert floating-ins.pg -G - > floating-ins2.gaf t/48_vg_convert.t ..... 1..26 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout ODGI conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - odgi conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 14 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 15 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 17 - vg convert gam -> gaf -> gam preserves sequence ok 18 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 19 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 20 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads not ok 21 - split alignment converted using deletions to represent internal offsets # got: '' # expected: 'cs:Z::13-CCAGTGCTC-GCATC:2' ok 22 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 23 - convert gam->gaf->gam on softclipped read preserves sequence ok 24 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 25 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment Failed 1/26 subtests t/49_vg_depth.t: line 10: 1199027 Illegal instruction (core dumped) vg construct -m 10 -r tiny/tiny.fa > flat.vg t/49_vg_depth.t: line 11: 1199028 Illegal instruction (core dumped) vg view flat.vg 1199029 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' 1199030 (core dumped) | vg view -Fv - > 2snp.vg t/49_vg_depth.t: line 12: 1199031 Illegal instruction (core dumped) vg sim -l 30 -x 2snp.vg -n 30 -a -s 1 > 2snp.sim t/49_vg_depth.t: line 13: 1199032 Illegal instruction (core dumped) vg index -x flat.xg -g flat.gcsa -k 16 flat.vg t/49_vg_depth.t: line 14: 1199033 Illegal instruction (core dumped) vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam t/49_vg_depth.t: line 15: 1199034 Illegal instruction (core dumped) vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam t/49_vg_depth.t ....... 1..4 not ok 1 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from gam' not ok 2 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from pack' not ok 3 - vg depth gets correct number of bins # got: '0' # expected: '5' not ok 4 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from gaf' Failed 4/4 subtests t/50_vg_giraffe.t: line 10: 1199051 Illegal instruction (core dumped) vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg t/50_vg_giraffe.t: line 11: 1199052 Illegal instruction (core dumped) vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg t/50_vg_giraffe.t: line 12: 1199053 Illegal instruction (core dumped) vg snarls --include-trivial x.vg > x.snarls t/50_vg_giraffe.t: line 13: 1199054 Illegal instruction (core dumped) vg index -s x.snarls -j x.dist x.vg t/50_vg_giraffe.t: line 14: 1199055 Illegal instruction (core dumped) vg minimizer -k 29 -w 11 -g x.gbwt -i x.min x.xg t/50_vg_giraffe.t: line 16: 1199056 Illegal instruction (core dumped) vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq > mapped1.gam t/50_vg_giraffe.t: line 19: 1199057 Illegal instruction (core dumped) vg minimizer -k 29 -b -s 18 -g x.gbwt -i x.sync x.xg t/50_vg_giraffe.t: line 21: 1199058 Illegal instruction (core dumped) vg giraffe -x x.xg -H x.gbwt -m x.sync -d x.dist -f reads/small.middle.ref.fq > mapped.sync.gam t/50_vg_giraffe.t: line 30: 1199063 Illegal instruction (core dumped) vg giraffe x.fa x.vcf.gz -f reads/small.middle.ref.fq > mapped2.gam t/50_vg_giraffe.t: line 35: 1199064 Illegal instruction (core dumped) vg view -aj mapped1.gam > mapped1.json t/50_vg_giraffe.t: line 36: 1199065 Illegal instruction (core dumped) vg view -aj mapped2.gam > mapped2.json t/50_vg_giraffe.t: line 37: 1199066 Illegal instruction (core dumped) vg view -aj mapped.sync.gam > mapped.sync.json t/50_vg_giraffe.t: line 54: 1199074 Illegal instruction (core dumped) vg giraffe x.fa x.vcf.gz -f small/x.fa_1.fastq > single.gam t/50_vg_giraffe.t: line 57: 1199079 Illegal instruction (core dumped) vg giraffe x.fa x.vcf.gz -f small/x.fa_1.fastq -f small/x.fa_1.fastq --fragment-mean 300 --fragment-stdev 100 > paired.gam t/50_vg_giraffe.t: line 61: 1199085 Illegal instruction (core dumped) vg giraffe x.fa x.vcf.gz -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG - ) --output-format SAM > surjected.sam t/50_vg_giraffe.t: line 61: 1199086 Illegal instruction (core dumped) vg view -a small/x-s13241-n1-p500-v300.gam 1199087 Done | sed 's%_1%/1%' 1199088 Done | sed 's%_2%/2%' 1199089 (core dumped) | vg view -JaG - t/50_vg_giraffe.t: line 69: 1199122 Illegal instruction (core dumped) vg view -a small/x-s13241-n1-p500-v300.gam 1199123 Done | sed 's%_1%/1%' 1199124 Done | sed 's%_2%/2%' 1199125 (core dumped) | vg view -JaG - t/50_vg_giraffe.t: line 69: 1199121 Illegal instruction (core dumped) vg giraffe x.fa x.vcf.gz -G <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG - ) --output-format SAM > surjected.sam t/50_vg_giraffe.t ..... 1..20 not ok 1 - a read can be mapped with all indexes specified without crashing # got: '132' # expected: '0' not ok 2 - a read can be mapped with syncmer indexes without crashing # got: '132' # expected: '0' not ok 3 - a read can be mapped with just FASTA and VCF without crashing # got: '132' # expected: '0' not ok 4 - mapping with just a FASTA and a VCF produced JSON-able alignments # got: '1' # expected: '0' ok 5 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 6 - mapping with syncmers produces the same alignment as mapping with minimizers not ok 7 - unpaired reads lack cross-references # got: '0' # expected: '1000' ok 8 - paired reads have cross-references not ok 9 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 10 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 11 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 12 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 13 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 14 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 15 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 16 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 17 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 18 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:y LN:1001 > @SQ SN:x LN:1001 not ok 19 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order # got: '1' # expected: '0' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:x LN:1001 > @SQ SN:y LN:1001 not ok 20 - surjecting with a sequence dictionary in sorted order produces headers in sorted order # got: '1' # expected: '0' Failed 17/20 subtests Test Summary Report ------------------- t/00_unittest.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/02_vg_construct.t (Wstat: 0 Tests: 28 Failed: 22) Failed tests: 1-6, 8-10, 12, 16-21, 23-28 t/03_vg_view.t (Wstat: 0 Tests: 19 Failed: 13) Failed tests: 1-4, 10-14, 16-19 t/04_vg_align.t (Wstat: 0 Tests: 20 Failed: 20) Failed tests: 1-20 t/05_vg_find.t (Wstat: 0 Tests: 27 Failed: 25) Failed tests: 1-14, 16-24, 26-27 t/06_vg_index.t (Wstat: 0 Tests: 51 Failed: 47) Failed tests: 1-10, 12-16, 18-21, 23-36, 38-51 t/07_vg_map.t (Wstat: 0 Tests: 54 Failed: 49) Failed tests: 1-14, 17-21, 24-31, 33-54 t/08_vg_ids.t (Wstat: 0 Tests: 10 Failed: 9) Failed tests: 1-5, 7-10 t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 2) Failed tests: 2, 4 t/10_vg_stats.t (Wstat: 0 Tests: 18 Failed: 17) Failed tests: 1-8, 10-18 t/11_vg_paths.t (Wstat: 0 Tests: 14 Failed: 12) Failed tests: 1-5, 7-12, 14 t/12_vg_kmers.t (Wstat: 0 Tests: 10 Failed: 10) Failed tests: 1-10 t/13_vg_sim.t (Wstat: 0 Tests: 34 Failed: 29) Failed tests: 1-5, 9-13, 15, 17-34 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 25) Failed tests: 2-11, 13-14, 16, 18-21, 24-25, 27-32 t/15_vg_surject.t (Wstat: 0 Tests: 33 Failed: 30) Failed tests: 1-13, 16-18, 20-33 t/16_vg_msga.t (Wstat: 0 Tests: 14 Failed: 12) Failed tests: 1-4, 7-14 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 31) Failed tests: 1-19, 22-23, 26-27, 29-30, 32-33, 35-36 38-39 t/18_vg_call.t (Wstat: 0 Tests: 12 Failed: 4) Failed tests: 2, 4-5, 11 t/20_vgtordf.t (Wstat: 0 Tests: 6 Failed: 4) Failed tests: 1-2, 5-6 t/21_vg_filter.t (Wstat: 0 Tests: 10 Failed: 4) Failed tests: 1-2, 5, 10 t/25_circularize.t (Wstat: 0 Tests: 2 Failed: 2) Failed tests: 1-2 t/26_deconstruct.t (Wstat: 0 Tests: 19 Failed: 17) Failed tests: 1-5, 7-18 t/27_vg_genotype.t (Wstat: 0 Tests: 5 Failed: 4) Failed tests: 1-2, 4-5 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/30_vg_chunk.t (Wstat: 0 Tests: 24 Failed: 14) Failed tests: 1-8, 10-13, 15-16 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 8) Failed tests: 1-2, 4, 7-8, 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 9 Failed: 5) Failed tests: 1-4, 8 t/33_vg_mpmap.t (Wstat: 256 Tests: 17 Failed: 16) Failed tests: 1-12, 14-17 Non-zero exit status: 1 t/34_vg_pack.t (Wstat: 0 Tests: 18 Failed: 7) Failed tests: 1-4, 10-11, 18 t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 7) Failed tests: 1-2, 5-9 t/37_vg_gbwt.t (Wstat: 0 Tests: 91 Failed: 90) Failed tests: 1-23, 25-91 t/38_vg_prune.t (Wstat: 0 Tests: 18 Failed: 18) Failed tests: 1-18 t/39_vg_inject.t (Wstat: 0 Tests: 10 Failed: 9) Failed tests: 1-9 t/40_vg_gamcompare.t (Wstat: 0 Tests: 5 Failed: 4) Failed tests: 1-3, 5 t/42_vg_gamsort.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/43_vg_simplify.t (Wstat: 0 Tests: 5 Failed: 5) Failed tests: 1-5 t/44_vg_benchmark.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/45_vg_sort.t (Wstat: 0 Tests: 5 Failed: 5) Failed tests: 1-5 t/46_vg_minimizer.t (Wstat: 0 Tests: 14 Failed: 14) Failed tests: 1-14 t/47_vg_dotplot.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/48_vg_convert.t (Wstat: 0 Tests: 26 Failed: 1) Failed test: 21 t/49_vg_depth.t (Wstat: 0 Tests: 4 Failed: 4) Failed tests: 1-4 t/50_vg_giraffe.t (Wstat: 0 Tests: 20 Failed: 17) Failed tests: 1-4, 7, 9-20 Files=49, Tests=758, 179 wallclock secs ( 0.88 usr 0.15 sys + 62.14 cusr 71.81 csys = 134.98 CPU) Result: FAIL Testing /build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-plain '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg-plain' -> '/build/vg-OlWF3C/vg-1.30.0+ds/debian/help/vg' ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yf0Tfs/stacktrace.txt Please include the stack trace file in your bug report! t/00_unittest.t ....... 1..1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vg test is a Catch v1.8.2 host application. Run with -? for options ------------------------------------------------------------------------------- We can convert a two-tailed graph to Cactus ------------------------------------------------------------------------------- src/unittest/cactus.cpp:16 ............................................................................... src/unittest/cactus.cpp:16: FAILED: due to a fatal error condition: SIGILL - Illegal instruction signal =============================================================================== test cases: 45 | 44 passed | 1 failed assertions: 7396 | 7395 passed | 1 failed not ok 1 - vg unit tests complete successfully # got: '132' # expected: '0' Failed 1/1 subtests t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! Restricting to gi|568815592:29791752-29792749 from 1 to end ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LaBjZ9/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error:[vg::Constructor] non-ATGCN characters found in variant: x 973 . G A,* 99 . AC=2;LEN=1;NA=2;NS=1;TYPE=snp warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. t/02_vg_construct.t ... 1..28 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges ok 7 - node size is manageable by default ok 8 - construction of a very complex region succeeds ok 9 - the complex graph has the expected number of nodes ok 10 - the complex graph has the expected number of edges ok 11 - the ordering of variants at the same position has no effect on the resulting graph ok 12 - construction does not fail when the first position in the VCF is repeated and has an indel ok 13 - the size of the regions used in construction has no effect on the graph ok 14 - the number of threads used in construction has no effect on the graph ok 15 - the number of threads and regions used in construction has no effect on the graph ok 16 - construction of a graph with two head nodes succeeds ok 17 - the graph contains all the sequence in the reference and VCF ok 18 - varying the max node size does not affect graph length ok 19 - nodes are correctly capped in size ok 20 - -R --region flag is respected ok 21 - vg construct does not require a vcf ok 22 - vg construct respects node size limit ok 23 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 24 - vg constructs the correct graph for inversions not ok 25 - vg construct skips variants with . ALTs # got: '' # expected: '1' ok 26 - VCF with * alleles is rejected ok 27 - Reference with ambiguity codes has them coerced to Ns ok 28 - Expected number of Ns are created Failed 1/28 subtests t/03_vg_view.t ........ 1..19 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM ok 5 - view can round-trip JSON and GAM ok 6 - view can reconstruct a VG graph from JSON ok 7 - view can pass through VG when loading as vg::VG ok 8 - view can pass through semantically identical VG normally ok 9 - view parses sample names ok 10 - view can handle fastq input ok 11 - view can translate graphs with 2-node cycles ok 12 - view outputs properly oriented GFA ok 13 - view produces the expected number of lines of dot output from a cyclic graph ok 14 - streaming JSON output produces the expected number of chunks ok 15 - duplicate warnings can be suppressed when loading as vg::VG ok 16 - gfa graphs with overlaps are rejected ok 17 - GFA import produces a concise error message when overlaps are present ok 18 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 19 - GFA import produces a concise error message in that case ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8XdkrY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3cSSiK/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_psUEAh/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ew4wQT/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_MvP01t/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_t3k99Y/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3ZDIxH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CMai2k/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_X1Qf4Y/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8AOnnB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CkIwWf/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_36KzSR/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_MF6pLt/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zWxhST/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BS3m5H/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_r24k1q/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TYejqQ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5pZ2yh/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_uHrL6I/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mP6Qze/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Sp57wL/stacktrace.txt Please include the stack trace file in your bug report! t/04_vg_align.t ....... 1..20 not ok 1 - alignment traverses the correct path # got: '0' # expected: '4' not ok 2 - unnamed test # got: '48' # expected: 'alignment score is as expected' not ok 3 - unnamed test # got: '58' # expected: 'full length bonus works and is included by default' not ok 4 - unnamed test # got: '37' # expected: 'bonuses are included on only one end for pinned alignments' not ok 5 - unnamed test # got: '96' # expected: 'scoring parameters are respected' not ok 6 - unnamed test # got: '96' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected' not ok 7 - unnamed test # got: '70211814' # expected: 'alignment does not contain excessive soft clips under lenient scoring' not ok 8 - unnamed test # got: '70211814' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring' not ok 9 - unnamed test # got: '274' # expected: 'alignment score does not overflow at 255 when using 8x16bit vectors' not ok 10 - unnamed test # got: '274' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors' not ok 11 - unnamed test # got: '280136076' # expected: 'Ns do not cause excessive soft clipping' not ok 12 - unnamed test # got: '59867694' # expected: 'nodes are only referenced if they have mappings' not ok 13 - align can use query names and outputs GAM # got: '0' # expected: '4' not ok 14 - alignment to cyclic graphs works # got: '0' # expected: '1' not ok 15 - graphs where duplicated nodes need flipping can be used for alignment # got: '132' # expected: '0' not ok 16 - node flipping doesn't destroy the alignment # got: '132' # expected: '0' not ok 17 - alignment correctly handles an inversion # got: '132' # expected: '0' not ok 18 - the exploding graph doesn't blow up # got: '132' # expected: '0' not ok 19 - unnamed test # got: '1' # expected: 'pinning doesn't cause problems for gssw' not ok 20 - unnamed test # got: '1' # expected: 'left pinning is correctly handled' Failed 20/20 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zP1osK/stacktrace.txt Please include the stack trace file in your bug report! t/05_vg_find.t: line 65: 1209613 Killed vg gamsort -i x.sorted.gam.gai x.gam > x.sorted.gam error:[get_input_file] could not open file "x.sorted.gam.gai" error:[get_input_file] could not open file "x.sorted.gam.gai" WARNING:[vg] Subcommand 'combine' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/05_vg_find.t ........ 1..27 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns not ok 16 - the GAM index can return the set of alignments mapping to a node # got: '0' # expected: '6' not ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM # got: '0' # expected: '15' ok 18 - the index can be queried using GAM alignments ok 19 - find gets connected edges between queried nodes by default ok 20 - find gets nodes provided in a node file list ok 21 - extracting by path adds no extra edges ok 22 - pattern based path extraction works ok 23 - path DAG range query works ok 24 - we can extract a set of targets to separate files ok 25 - the same extraction can be made using BED input ok 26 - we see the expected number of kmers in the given targets ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 Failed 2/27 subtests t/06_vg_index.t: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8): No such file or directory WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JQBkhK/stacktrace.txt Please include the stack trace file in your bug report! t/06_vg_index.t: line 183: 1218200 Segmentation fault (core dumped) vg map -T <(vg sim -n 100 -x x.xg) -d x > x1337.gam t/06_vg_index.t: line 186: 1218238 Killed vg gamsort -i x1337.sorted.gam.gai2 x1337.gam > x1337.sorted.gam t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_uP8ax0/stacktrace.txt Please include the stack trace file in your bug report! t/06_vg_index.t ....... 1..51 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - samples can be excluded from haplotype indexing ok 19 - excluded samples were not included in the GBWT index ok 20 - GBWT from GAF same as from GAM ok 21 - building GBWT index for a regional graph ok 22 - no warnings about missing variants produced ok 23 - building an XG index of multiple graphs ok 24 - building a GCSA index of multiple graphs ok 25 - building both indexes at once ok 26 - the indexes are identical ok 27 - building a GBWT index of multiple graphs with haplotypes ok 28 - building an XG index of multiple graphs with haplotypes ok 29 - building a GCSA index of multiple graphs with haplotypes ok 30 - building XG and GCSA indexes at once ok 31 - building an XG index with alt paths ok 32 - building a GBWT index from an XG index ok 33 - the indexes are identical ok 34 - GBWT can be built for paths ok 35 - fail with nonexistent file ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used not ok 37 - vg index and vg gamsort produce identical sorted GAM indexes # got: 'c4904818dcce89724c9cef7541356be3 -' # expected: '' ok 38 - storage of multiple graphs in an index succeeds ok 39 - can index backward nodes ok 40 - can index kmers for backward nodes ok 41 - GCSA2 index works on cyclic graphs with heads and tails ok 42 - GCSA2 index works on cyclic graphs with no heads or tails ok 43 - GCSA2 index works on cyclic graphs with self loops ok 44 - GCSA2 index works on general cyclic graphs ok 45 - GCSA2 indexing of a tiny graph works ok 46 - GCSA2 indexing succeeds on a single-node graph ok 47 - GCSA2 indexing succeeds on graph with heads but no tails ok 48 - a useful error message is produced when nodes are too large not ok 49 - snarl finding with trivial snarls # got: '132' # expected: '0' ok 50 - building a distance index of a graph ok 51 - building a distance index of a graph without maximum index Failed 2/51 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_EF79RM/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_IZAvNG/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2ody8v/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_usFq4q/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Cb61ij/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HRpi39/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CikOYd/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5H1IN7/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_IbOqJY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_j09jWR/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CPxfFM/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dC0ssy/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Bp7p2l/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LhA2DH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_s9xafO/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ODbfqN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oXvJZR/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cUKGgJ/stacktrace.txt Please include the stack trace file in your bug report! printf: usage: printf [-v var] format [arguments] ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VsbBp5/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9lrRjL/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_j8rmB7/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7M3j18/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_84R5u8/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NV3Lbt/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_D7IPG1/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_a12Snf/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kejh0C/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_C8ELLB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HgQekF/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XjQdnr/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hInB9S/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JLWhlV/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PAyAcS/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BDrLtc/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WS761i/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_w2hwna/stacktrace.txt Please include the stack trace file in your bug report! [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1dsZuO/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xP7UDL/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_wNvgWK/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vrgfOF/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_adrXlB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ONuWj5/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Qj2o1W/stacktrace.txt Please include the stack trace file in your bug report! index file t.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gMLA0S/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7nUvqe/stacktrace.txt Please include the stack trace file in your bug report! t/07_vg_map.t ......... 1..54 not ok 1 - offset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 2 - xdrop alignment obtains the expected result # got: '' # expected: '3' not ok 3 - xdrop alignment obtains the expected result for the reverse complement # got: '' # expected: '5' not ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 5 - offset counts unused bases from the start of the node on the reverse strand # got: '' # expected: '5' not ok 6 - global alignment traverses the correct path # got: '0' # expected: '4' not ok 7 - alignment score is as expected # got: '' # expected: '58' not ok 8 - scoring parameters are respected # got: '' # expected: '106' not ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected # got: '' # expected: '106' not ok 10 - full length bonus always be included # got: '' # expected: '58' not ok 11 - full length bonus can be set to 0 # got: '' # expected: '96' not ok 12 - vg map takes -d as input without a variant graph # got: '132' # expected: '0' not ok 13 - vg map can align across a SNP # got: '0' # expected: '1' not ok 14 - alignment works on a small graph # got: '0' # expected: '1000' ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities not ok 17 - chunky-banded alignment works # got: '0' # expected: '1' not ok 18 - unnamed test # got: '' # expected: 'multiple alignments are returned in descending score order' not ok 19 - only a single primary alignment is returned # got: '0' # expected: '1' not ok 20 - mapping of BAM file produces expected number of alignments # got: '0' # expected: '3333' not ok 21 - mapping from a fastq produces the expected number of alignments # got: '0' # expected: '3327' ok 22 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 23 - vg connects paired-end reads in gam output not ok 24 - mapping to graphs that can't be oriented without swapping edges works correctly # got: '132' # expected: '0' not ok 25 - reads multi-map to multiple possible locations # got: '0' # expected: '1' not ok 26 - vg map works based on gcsa and xg indexes # got: '0' # expected: '1000' not ok 27 - unnamed test # got: '30' # expected: 'the mapping quality may be capped' not ok 28 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 29 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 30 - only primary alignments have mapping quality scores # got: '0' # expected: '2' not ok 31 - unpaired reads produce mapping quality scores # got: '0' # expected: '1000' ok 32 - map returns same output on xg and vg (single threaded) not ok 33 - unnamed test # got: '10' # expected: 'base quality adjusted alignment produces higher scores if mismatches have low quality' ok 34 - error on vg map -f (unpaired) ok 35 - error on vg map -f (interleaved) ok 36 - error on vg map -f (paired, LHS) ok 37 - error on vg map -f (paired, RHS) not ok 38 - mapping a read that touches unused nodes gets the base score # got: '' # expected: '36' not ok 39 - mapping a read that matches a haplotype gets a small penalty # got: '' # expected: '35' not ok 40 - mapping a read that matches a haplotype with exponent 0 gets the base score # got: '' # expected: '36' not ok 41 - mapping a read that matches no haplotypes gets a larger penalty # got: '' # expected: '21' not ok 42 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 43 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 44 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 45 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 46 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 47 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 48 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 49 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 50 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 51 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' not ok 52 - unnamed test # got: '1' # expected: 'mapper can read FASTA input' not ok 53 - unnamed test # got: '1' # expected: 'mapper can read multiline FASTA input' not ok 54 - unnamed test # got: '130' # expected: 'xdrop works on a reversed read' Failed 45/54 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3W0lTu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YRzwFB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kiPKCJ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aHXsba/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dBts6s/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cBc7t5/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7wOxoI/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs not ok 4 - can sort and re-number a graph with self loops # got: '132' # expected: '0' not ok 5 - can sort and renumber a complex cyclic graph # got: '132' # expected: '0' ok 6 - sorting removes back-edges in a DAG not ok 7 - unnamed test # got: 'true' # expected: 'sorting assigns node IDs in topological order' not ok 8 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range' not ok 9 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range of vg' not ok 10 - unnamed test # got: '1:3' # expected: 'sorting does not affect id range of hg' Failed 6/10 subtests t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes ok 2 - concat doubles the number of edges + 1 ok 3 - concat -p doubles the number of nodes on reversing graph ok 4 - concat -p doubles the number of edges + 1 on reversing graph ok t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lwfUxf/stacktrace.txt Please include the stack trace file in your bug report! t/10_vg_stats.t: line 40: 1226829 Segmentation fault (core dumped) vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam t/10_vg_stats.t ....... 1..18 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct not ok 8 - aligned read stats are computed correctly # got: '1b5d954befa462c8f6bd2bfdc6dcbf91' # expected: 'b45c940480441a36475217a41b35e1f6' ok 9 - basic stats agree between graph formats not ok 10 - stats can be computed for GAM files without graphs # got: 'Total alignments: 0' # expected: 'Total alignments: 100' ok 11 - a path overlap description of a test graph has the expected length ok 12 - vg stats -F detects format of old protobuf graph ok 13 - vg stats -F detects format of newer protobuf graph ok 14 - vg stats -F detects format of hash graph ok 15 - vg stats -F detects format of packed graph ok 16 - vg stats -F detects format of odgi graph ok 17 - vg stats -F detects format of xg graph ok 18 - vg stats -D found correct degree distribution of tiny graph Failed 2/18 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NineqU/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Iy48zC/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mCS3I7/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/11_vg_paths.t ....... 1..14 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - thread listing works from GBWT ok 4 - thread selection by name prefix works correctly ok 5 - thread selection by sample name works correctly ok 6 - no threads are reported for invalid samples ok 7 - vg paths may be used to extract threads ok 8 - vg paths may be used to extract threads as GAF ok 9 - Fasta extracted from xg is the same as the input fasta ok 10 - Fasta extracted from vg is the same as the input fasta ok 11 - Fasta extracted from threads has correct number of lines not ok 12 - a single path may be retained # got: '0' # expected: '1' ok 13 - path filtering does not modify the graph ok 14 - alt allele paths can be dropped Failed 1/14 subtests WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz t/13_vg_sim.t ......... 1..34 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - reads can be simulated from all paths ok 10 - simulation was successful ok 11 - reads can be simulated from GBWT samples ok 12 - simulation was successful ok 13 - pairs simulated even when fragments overlap ok 14 - sim does not emit reads with Ns ok 15 - sim can emit reads with Ns when asked to ok 16 - sim doesn't emit Ns even with pair and errors ok 17 - Sample simulation works along with --any-path ok 18 - not having any regexes skips all unvisited contigs ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig ok 22 - multiple regexes are interpreted ok 23 - regexes are interpreted as regexes ok 24 - assigning a very high ploidy by regex starves out the other paths ok 25 - Sample simulation works along with --any-path with training FASTQ ok 26 - not having any regexes skips all unvisited contigs with training FASTQ ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ ok 30 - multiple regexes are interpreted with training FASTQ ok 31 - regexes are interpreted as regexes with training FASTQ ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ ok 33 - ngs trained simulator works ok 34 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_88o07z/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Fc2Pr3/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_LyifIj/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_EcolHs/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3ZMaMF/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XRXZnT/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ov1uHe/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yWY6ef/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_38uVjF/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GrfWnZ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NBDcnr/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_FvPS4y/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. error[VPKG::load_one]: Correct input type not found in s.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_c3NaVQ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NWtjK7/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_tmwF8f/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KWATJd/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gZL3xC/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in /dev/fd/63 while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works not ok 5 - normalization produces the correct number of nodes # got: '0' # expected: '4' not ok 6 - normalization removes redundant SNP alleles # got: '0' # expected: '4' not ok 7 - normalization produces a valid graph # got: '1' # expected: '0' not ok 8 - looped normalization produces a valid graph # got: '1' # expected: '0' not ok 9 - unchop produces a valid graph # got: '1' # expected: '0' not ok 10 - unnamed test # got: '154' # expected: 'normalization removes redundant sequence in the graph' not ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '5d3999dfcafb09801e4659c1b43a8593' ok 12 - vg mod removes non-path nodes and edge ok 13 - chopping a graph works correctly with reverse mappings not ok 14 - unnamed test # got: '2f785068c91dbe84177c1fd679b6f133' # expected: 'unchop correctly handles paths' ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion not ok 18 - mod successfully unchops a difficult graph # got: '1' # expected: '0' not ok 19 - chopping self-cycling nodes retains the cycle # got: '1' # expected: '0' not ok 20 - unrolling works and produces a valid graph # got: '1' # expected: '0' not ok 21 - unfolding works and produces a valid graph # got: '1' # expected: '0' ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components not ok 25 - unfold followed by dagify produces a graph with no cycles # got: '0' # expected: '46' ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths not ok 29 - unnamed test # got: '4' # expected: 'dagify correctly calculates the minimum distance through the unrolled component' not ok 30 - unnamed test # got: '200' # expected: 'dagify produces a graph of the correct size' ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 16/32 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_O2iLip/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_MJ1khc/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zrC781/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Gpgv3f/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6js5Cr/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sCqgMV/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_iqC4EB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XkqnI3/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_FE9oAb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6CHpKY/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph Error[vg map]: Unable to open xg file "f.xg" error[VPKG::load_one]: Could not open f.xg while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rfByDD/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open Error[vg map]: Unable to open xg file "f.xg" f.xg while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_UjzdZH/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_QJC07i/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_3NjSiU/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_xLvWCB/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ouuaRm/stacktrace.txt Please include the stack trace file in your bug report! [main_samview] fail to read the header from "-". t/15_vg_surject.t ..... 1..33 not ok 1 - reads are generated # got: '0' # expected: '100' not ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 4 - vg surject actually places reads on the correct path # got: '0' # expected: '100' not ok 5 - vg surject doesn't need to be told which path to use # got: '0' # expected: '100' not ok 6 - vg surject works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 7 - vg surject spliced algorithm works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 8 - vg surject produces valid SAM output # got: '0' # expected: '100' not ok 9 - vg map may surject reads to produce valid SAM output # got: '0' # expected: '100' not ok 10 - vg map may surject reads to produce valid BAM output # got: '0' # expected: '100' not ok 11 - vg surject retains read names # got: '0' # expected: '100' not ok 12 - vg surject can set sample and read group # got: '0' # expected: '100' not ok 13 - we respect the original mapping's softclips # got: '0' # expected: '1' ok 14 - quality strings we will use for testing are oriented correctly ok 15 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags not ok 16 - vg surject produces valid BAM output # got: '0' # expected: '100' ok 17 - mapping quality is preserved through surjection ok 18 - read pairing is preserved through GAM->GAM surjection ok 19 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 25 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 26 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' not ok 27 - surjection works for a longer (151bp) read # got: '0' # expected: '1' not ok 28 - surjection works for another difficult read # got: '0' # expected: '1' not ok 29 - mapping reproduces qualities from BAM input # got: '0' # expected: '1' not ok 30 - mapping reproduces qualities from fastq input # got: '0' # expected: '1' not ok 31 - mapping reproduces qualities from GAF input # got: '0' # expected: '1' not ok 32 - surject works on GAMP input # got: '0' # expected: '1000' not ok 33 - surject works on paired GAMP input # got: '0' # expected: '1000' Failed 28/33 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JHpmbe/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_p0DXHV/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8RBwiC/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9pMlz7/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_APErjo/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ewdYHc/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. error[VPKG::load_one]: Correct input type not found in s.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_S93tD3/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DGNvwr/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_b6c3KD/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Bkz0aK/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JqtS30/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_FEN5un/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Z5Ps4x/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VKciSH/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/16_vg_msga.t ........ 1..14 not ok 1 - MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '16e56f0090b310d2b1479d49cf790324' not ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '2ab075dd73c31ea9939726d72c12655f' not ok 3 - soft clips at node boundaries (start) are included correctly # got: '0' # expected: '1' not ok 4 - soft clips at node boundaries (end) are included correctly # got: '0' # expected: '1' ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph not ok 7 - the paths of the graph encode the original sequences used to build it # got: '0' # expected: '2' not ok 8 - even when banding the paths of the graph encode the original sequences used to build it # got: '1' # expected: '0' not ok 9 - HLA K-3138 correctly includes all input paths # got: '1' # expected: '0' not ok 10 - a difficult cyclic path can be included to produce a valid graph # got: '1' # expected: '0' not ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected # got: '0' # expected: '1' not ok 12 - edges in cycles with two nodes are correctly included # got: '1' # expected: '0' not ok 13 - HLA B-3106 is assembled into a valid graph # got: '1' # expected: '0' not ok 14 - odd-sized overlaps may be used for chunked alignment # got: '1' # expected: '0' Failed 12/14 subtests [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aGho4a/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TAeU86/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Ch8If0/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_kxPGQs/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ixiVZq/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_auFbGw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1IwjqB/stacktrace.txt Please include the stack trace file in your bug report! Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_UHIyTX/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XMgW1v/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7vsp6N/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dXJvaN/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vC7QJY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_OXEIqC/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1wcuU1/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_VLDhOe/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BVqQhI/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Ybz9ol/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_eiP5kw/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TtCHUX/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_CoKc6w/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TU7nrN/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_N6aEto/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6TlMr8/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HsXXsl/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_uGdUb1/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gWVl3G/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_mLeLIu/stacktrace.txt Please include the stack trace file in your bug report! t/17_vg_augment.t ..... 1..39 ok 1 - direct augmentation embeds reads fully for well-supported SNPs ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes ok 6 - direct augmentation embeds reads fully for probable errors ok 7 - adding a probable error by direct augmentation adds 3 more nodes ok 8 - path inclusion does not modify the graph when alignment is a perfect match ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold not ok 11 - output GAM has single edit when SNP was filtered out due to coverage # got: '0' # expected: '1' not ok 12 - path inclusion with a complex variant introduces the right number of nodes # got: '1' # expected: '5' not ok 13 - path inclusion works for deletions # got: '0' # expected: '1' not ok 14 - SNPs can be included in the graph # got: '1' # expected: '4' not ok 15 - unnamed test # got: 'GGGGG' # expected: 'a soft clip at read start becomes a new head of the graph' not ok 16 - unnamed test # got: 'AAAAAAAA' # expected: 'a soft clip at read end becomes a new tail of the graph' not ok 17 - augment -s works as desired # got: '0' # expected: '1' not ok 18 - the expected graph translation is exported when the graph is edited # got: '420' # expected: '1290' not ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes # got: '0' # expected: '7' ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps not ok 22 - augmenting with 2snps makes correct number of nodes # got: '1' # expected: '7' not ok 23 - low-quality snp is filtered # got: '1' # expected: '4' ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph 2a3 > GGNGG not ok 26 - augmenting between nodes without filters works as expected # got: '1' # expected: '0' 2a3 > GGNGG not ok 27 - augmenting between nodes with inactive filters works as expected # got: '1' # expected: '0' ok 28 - augmenting between nodes N filter works as expected 2a3 > GGNGG not ok 29 - augmenting between nodes without filters works as expected on reverse strand # got: '1' # expected: '0' 2a3 > GGNGG not ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand # got: '1' # expected: '0' ok 31 - augmenting between nodes N filter works as expected on reverse strand not ok 32 - augmenting within node without filters works as expected # got: '0' # expected: '1' not ok 33 - augmenting within node with inactive filters works as expected # got: '0' # expected: '1' ok 34 - augmenting within node with N filter works as expected not ok 35 - augmenting within node without filters works as expected on reverse strand # got: '0' # expected: '1' not ok 36 - augmenting within node with inactive filters works as expected on reverse strand # got: '0' # expected: '1' ok 37 - augmenting within node with N filter works as expected on reverse strand not ok 38 - unnamed test # got: 'CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG' # expected: 'sequence in filtered alignment has removed insertion' not ok 39 - unnamed test # got: 'CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG' # expected: 'sequence in filtered alignment has removed insertion on reverse strand' Failed 21/39 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lmKAvN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_X9f457/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_7ulMxj/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_l9zGeA/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_dNTymK/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1vYEc3/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_olOSUz/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9blwec/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_x8SsJ7/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5c7CuY/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cmHdLr/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HZmCai/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_EPODlX/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph Error[vg map]: Unable to open xg file "c.xg" error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open c.aug.xg while loading handlegraph::HandleGraph error:[get_input_file] could not open file "c.aug.xg" ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_eabNSg/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ElTk9j/stacktrace.txt Please include the stack trace file in your bug report! t/18_vg_call.t ........ 1..12 ok 1 - calling empty gam gives empty VCF not ok 2 - Called microinversion # got: '0' # expected: '1' ok 3 - Called no microinversion with haploid setting not ok 4 - Fewer than 8 differences between called and true SV genotypes # got: '0' # expected: '1' not ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes # got: '0' # expected: '1' ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg not ok 11 - vg call finds true homozygous variants in a cyclic graph # got: '0' # expected: '3' ok 12 - vg call finds same variants when using gbwt to enumerate traversals Failed 4/12 subtests t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok t/21_vg_filter.t ...... 1..10 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - read pairs can be tropped by feature ok 10 - read pairs can be kept if only one read fails ok t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4jQeWi/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_vkPN24/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "hla.xg" error:[get_input_file] could not open file "hla.xg" error:[get_input_file] could not open file "hla.xg" ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_L2ZU6H/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WsNNxw/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_bZM6w0/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_HErEkN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Y7wus0/stacktrace.txt Please include the stack trace file in your bug report! graph path 'alt2.3' invalid: edge from 15 end to 1 start does not exist [vg view] warning: graph is invalid! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4UgaSN/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cNnz7m/stacktrace.txt Please include the stack trace file in your bug report! t/26_deconstruct.t .... 1..19 1,3d0 < x 14 G A < x 34 T A < x 39 T A not ok 1 - deconstruct retrieved original VCF (modulo adjacent snp allele) # got: '1' # expected: '0' not ok 2 - deconstructed hla vcf has correct number of sites # got: '0' # expected: '17' not ok 3 - unnamed test # got: 'C-CGCGGGCGCCGTGGATGGAGCA' # expected: 'deconstructed hla vcf has correct insertion' not ok 4 - deconstructed hla vcf with other path has correct number of sites # got: '0' # expected: '17' not ok 5 - unnamed test # got: 'CGCGGGCGCCGTGGATGGAGCA-C' # expected: 'deconstructed hla vcf has correct deletion' ok 6 - path-based and exhaustive decontruction give equivalent sites when expected not ok 7 - unnamed test # got: '1' # expected: 'path that differs from reference in every alt has correct genotype' not ok 8 - unnamed test # got: '0' # expected: 'path that is same as reference in every alt has correct genotype' not ok 9 - unnamed test # got: '##contig=' # expected: 'reference contig correctly written' 0a1 > x 10 CTTGGAAATTTTCTGGAGTT AACTCCAGAAAATTTCCAAG 1 not ok 10 - deconstruct correctly handles a simple inversion # got: '1' # expected: '0' 0a1 > y 10 AACTCCAGAAAATTTCCAAG CTTGGAAATTTTCTGGAGTT 1 not ok 11 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge # got: '1' # expected: '0' 0a1 > y 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA 1 not ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl # got: '1' # expected: '0' 0a1 > x 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA 1 not ok 13 - deconstruct correctly handles a cycle in the alt path # got: '1' # expected: '0' not ok 14 - cyclic reference deconstruction has correct number of variants # got: '0' # expected: '2' 0a1,2 > y 20 T A 0 > y 44 A T 1 not ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl # got: '1' # expected: '0' not ok 16 - -P -A options return correct number of variants # got: '0' # expected: '2' not ok 17 - -P -A options use correct reference name # got: '0' # expected: '2' not ok 18 - -P -A identifies conflict in alt1 in second variant # got: '0' # expected: '1' ok 19 - deconstructing vg graph gives same output as xg graph Failed 17/19 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_fyraA0/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t: line 14: 1299509 Segmentation fault (core dumped) vg map -T reads.txt -g tiny.vg.gcsa -x tiny.vg.xg > tiny.gam ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cRhrpG/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KHxxVJ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TOQo9X/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Wuj5cL/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file flats.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_v1S2fV/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WW8eRn/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yNAwKC/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t: line 54: 1301462 Segmentation fault (core dumped) vg map -T reads.txt -g bigins.vg.gcsa -x bigins.vg.xg > bigins.gam ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Kg9QEp/stacktrace.txt Please include the stack trace file in your bug report! t/27_vg_genotype.t .... 1..5 not ok 1 - vg genotype runs successfully # got: '132' # expected: '0' not ok 2 - vg genotype runs successfully when emitting vcf # got: '132' # expected: '0' ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON not ok 5 - genotype finds big insert # got: '0' # expected: '1' Failed 3/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pJHuty/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_00FaUV/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_JFxNhD/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_TNldUE/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PFYaMz/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end t/30_vg_chunk.t ....... 1..24 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk has path going through node 9 ok 5 - -s produces correct number of chunks ok 6 - gam chunker produces correct number of graphs ok 7 - gam chunker produces correct number of gams ok 8 - gam chunker produces bed with correct number of chunks ok 9 - gam chunker emits each matching read at most once ok 10 - chunk contains the expected number of alignments ok 11 - id chunker produces correct chunk size ok 12 - id chunker produces correct single chunk ok 13 - id chunker traces correct chunk size ok 14 - chunker extracts no threads from an empty gPBWT ok 15 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 16 - chunker can extract a partial haplotype from a GBWT ok 17 - n-chunking works and chunks over the full graph ok 18 - path-based components finds subgraphs ok 19 - x gam chunk has correct number of reads ok 20 - y gam chunk has correct number of reads ok 21 - x gam chunk has correct number of reads with -p path ok 22 - y gam chunk has correct number of reads with -p path ok 23 - path-based component contains correct path length ok 24 - components finds subgraphs ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_22hQjZ/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0rAc9n/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gZ1bl1/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_We2EWr/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XhfUMY/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_45yYl3/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in ngap-add.vg while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_WEvsnu/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_lmXdwm/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_14aic6/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nJafzM/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..12 not ok 1 - vg add can create a graph # got: '132' # expected: '0' not ok 2 - vg add can create a graph with contig renames # got: '132' # expected: '0' ok 3 - vg add produces the same graph from VCFs with different contig names not ok 4 - vg add can create a graph from a PackedGraph # got: '132' # expected: '0' ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology not ok 7 - adding variants adds only the alt bases near large N gaps # got: '' # expected: '73315' not ok 8 - vg add can create a slightly larger graph # got: '132' # expected: '0' ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 8/12 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XGyRqF/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2504lT/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DDJtZV/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_YFRKQ5/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_2WzOPR/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_15FOp3/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_9mWmTM/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1qcbWX/stacktrace.txt Please include the stack trace file in your bug report! Restricting to x from 1 to end Restricting to y from 1 to end ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KlCjVP/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1pE8L2/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yFYLpm/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_5xtbsw/stacktrace.txt Please include the stack trace file in your bug report! t/32_vg_snarls.t ...... 1..9 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 4 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 5 - vcf traversals are the same as exhaustive traversals for tiny graph ok 6 - vcf traversals are the same as exhaustive traversals for inversion ok 7 - vcf traversals are the same as exhaustive traversals for ins_and_del graph not ok 8 - correct number of snarls when parallelizing on compoents # got: '0' # expected: '35' ok 9 - same number of snarls when parallelizing on components Failed 5/9 subtests [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 1.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 1.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.match.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Pxbw9t/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.match.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_DqZzTv/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.matchpaired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_AdXn3B/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.matchpaired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_bLDVcB/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pu4Iu7/stacktrace.txt Please include the stack trace file in your bug report! t/33_vg_mpmap.t: line 36: 1314839 Segmentation fault (core dumped) vg snarls xy2.vg > xy2.snarls warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GAw2Sd/stacktrace.txt Please include the stack trace file in your bug report! warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_pVT4dg/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from reads/xy2.discordant.fq using 1 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8gEF9d/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -P 1 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0.0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/xy2.discordant.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_qibJj3/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 10 -D 50 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_cEACi7/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -I 100000 -D 5 -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 1.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 1.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 1.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_rWHt41/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -B -i -F GAM [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_p2SAiS/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0.0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1.0 s: Mapping reads from input.gam using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_l92vif/stacktrace.txt Please include the stack trace file in your bug report! t/33_vg_mpmap.t: line 66: 1317406 Segmentation fault (core dumped) vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -i -F GAM --no-qual-adjust > output.gam [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -B -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0.0 s: Loading graph from t.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0.0 s: Mapping reads from t.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XStQ5R/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_XHPuJW/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_Kqtwb6/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_sE03ag/stacktrace.txt Please include the stack trace file in your bug report! [vg mpmap] elapsed time 0.0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 [vg mpmap] elapsed time 0.0 s: Loading graph from s.xg [vg mpmap] elapsed time 0.0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0.0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0.0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0.0 s: Loading distance index from s.dist [vg mpmap] elapsed time 1.0 s: Mapping reads from s.fq using 32 threads ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_z8S2ir/stacktrace.txt Please include the stack trace file in your bug report! t/33_vg_mpmap.t ....... 1..17 not ok 1 - MAPQ is 50% without haplotype info # got: '' # expected: '3' not ok 2 - haplotype match can disambiguate # got: '' # expected: '4' not ok 3 - MAPQ is 50% when paired without haplotype info # got: '' # expected: '3' not ok 4 - haplotype match can disambiguate paired # got: '' # expected: '4' not ok 5 - use of haplotype-aware mapping is recorded # got: '' # expected: 'true' not ok 6 - Haplotype-oblivious mapping places read on the wrong contig # got: '' # expected: '50' not ok 7 - Haplotype-oblivious mapping places read with MAPQ of 50% # got: '' # expected: '3' not ok 8 - Haplotype-aware mapping places read on the right contig # got: '' # expected: '1' not ok 9 - Haplotype-aware mapping places read with MAPQ > 50% # got: '' # expected: '6' not ok 10 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 11 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 12 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart # got: '0' # expected: '1' ok 13 - small batches are still all paired in the output not ok 14 - multipath mapping works in scenarios that trigger branch point trimming # got: '0' # expected: '3' not ok 15 - spliced alignments can be found when aligning RNA # got: '' # expected: '108' not ok 16 - paired mapping can identify a splice junction on read 1 # got: '0' # expected: '1' not ok 17 - paired mapping can identify a splice junction on read 2 # got: '0' # expected: '1' Failed 16/17 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_BUdJQU/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NK9GXy/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_GnSiMR/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_NnTTpf/stacktrace.txt Please include the stack trace file in your bug report! t/34_vg_pack.t ........ 1..18 not ok 1 - allele observation packing detects 2 SNPs # got: '0' # expected: '2' ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - average node qualities are correct # got: '0-0-0-0-0-0-0-0-0-0-' # expected: '20-15-10-10-0-0-0-0-60-60-' Failed 2/18 subtests t/36_vg_annotate.t .... 1..9 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature ok 7 - annotating with earliest path position produces one position ok 8 - annotating with multiple path positions produces multiple positions ok 9 - annotations derived from BED can span the end/start joins of circular paths ok t/37_vg_gbwt.t ........ 1..91 ok 1 - chromosome X GBWT with vg gbwt ok 2 - chromosome X GBWT with vg index ok 3 - identical construction results with vg gbwt and vg index ok 4 - chromosome X VCF parse ok 5 - chromosome X GBWT from VCF parse ok 6 - identical construction results with vg gbwt and from VCF parse ok 7 - chromosome X: 2 threads ok 8 - chromosome X: 1 contig ok 9 - chromosome X: 2 haplotypes ok 10 - chromosome X: 1 sample ok 11 - chromosome X: 2 thread names ok 12 - chromosome X: 1 contig name ok 13 - chromosome X: 1 sample name ok 14 - chromosome X reference GBWT with vg gbwt ok 15 - chromosome X reference GBWT with vg index ok 16 - identical construction results with vg gbwt and vg index ok 17 - chromosome X reference: 1 thread ok 18 - chromosome X GAF with vg gbwt ok 19 - chromosome X GAF with vg index ok 20 - identical construction results with vg gbwt and vg index ok 21 - chromosome X GAM with vg gbwt ok 22 - identical construction results from GAF and GAM ok 23 - chromosome X subgraph GBWT with vg gbwt ok 24 - no warnings about missing variants ok 25 - chromosome X subgraph GBWT with vg index ok 26 - identical construction results with vg gbwt and vg index ok 27 - insertion merging with multiple chromosomes ok 28 - fast merging with multiple chromosomes ok 29 - identical merging results with the insertion and fast algorithms ok 30 - parallel merging with multiple chromosomes ok 31 - identical merging results with the insertion and parallel algorithms ok 32 - direct construction with multiple chromosomes and a single VCF ok 33 - identical results with direct construction and merging ok 34 - direct construction with multiple chromosomes and multiple VCFs ok 35 - identical construction results with a single VCF and multiple VCFs ok 36 - construction preset: 1000gp ok 37 - multiple chromosomes: 4 threads ok 38 - multiple chromosomes: 2 contigs ok 39 - multiple chromosomes: 2 haplotypes ok 40 - multiple chromosomes: 1 sample ok 41 - paths as contigs with vg gbwt ok 42 - paths as contigs with vg index ok 43 - identical construction results with vg gbwt and vg index ok 44 - paths as contigs: 2 threads ok 45 - paths as contigs: 2 contigs ok 46 - paths as contigs: 1 haplotype ok 47 - paths as contigs: 1 sample ok 48 - paths as samples with vg gbwt ok 49 - paths as samples with vg index ok 50 - paths as samples: 2 threads ok 51 - paths as samples: 1 contig ok 52 - paths as samples: 2 haplotypes ok 53 - paths as samples: 2 samples ok 54 - r-index construction ok 55 - normal merging: non-empty + empty ok 56 - the index remains unchanged ok 57 - normal merging: empty + non-empty ok 58 - the index remains unchanged ok 59 - fast merging: non-empty + empty ok 60 - the index remains unchanged ok 61 - fast merging: empty + non-empty ok 62 - the index remains unchanged ok 63 - parallel merging: non-empty + empty ok 64 - the index remains unchanged ok 65 - parallel merging: empty + non-empty ok 66 - the index remains unchanged ok 67 - haplotypes and paths: 6 threads ok 68 - samples can be removed from a GBWT index ok 69 - haplotypes only: 4 threads ok 70 - threads can be extracted from GBWT ok 71 - correct size for the thread file ok 72 - GBWTGraph construction was successful ok 73 - GBWTGraph was correctly serialized ok 74 - Path cover GBWTGraph construction was successful ok 75 - GBWTGraph was correctly serialized ok 76 - path cover: 32 threads ok 77 - path cover: 2 contigs ok 78 - path cover: 16 haplotypes ok 79 - path cover: 16 samples ok 80 - Local haplotypes GBWTGraph construction was successful ok 81 - GBWTGraph was correctly serialized ok 82 - local haplotypes: 32 threads ok 83 - local haplotypes: 2 contigs ok 84 - local haplotypes: 16 haplotypes ok 85 - local haplotypes: 16 samples ok 86 - Augmented GBWTGraph construction was successful ok 87 - GBWTGraph was correctly serialized ok 88 - augmented: 18 threads ok 89 - augmented: 2 contigs ok 90 - augmented: 2 haplotypes ok 91 - augmented: 17 samples ok t/38_vg_prune.t ....... 1..18 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - empty mapping starts from the right node id ok 17 - the first unfolded graph adds the correct number of nodes to the mapping ok 18 - the second unfolded graph adds the correct number of nodes to the mapping ok t/39_vg_inject.t ...... 1..10 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_yiRW6p/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_6gpzCr/stacktrace.txt Please include the stack trace file in your bug report! 1000 reads correct ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_nhZ9xA/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_h6i5ui/stacktrace.txt Please include the stack trace file in your bug report! 0 reads correct 0 reads correct 0 reads correct t/40_vg_gamcompare.t .. 1..5 not ok 1 - gamcompare completes # got: '0' # expected: '1000' ok 2 - gamcompare says the truth is correctly mapped not ok 3 - Reads annotated with leftmost position only are close enough at a long distance # got: '0' # expected: '1' ok 4 - Reads annotated with leftmost position only are too far apart at a short distance not ok 5 - Reads annotated with multiple positions only are close enough at a short distance # got: '0' # expected: '1' Failed 3/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_50QNGM/stacktrace.txt Please include the stack trace file in your bug report! t/41_vg_viz.t ......... 1..1 ok 1 - vg viz runs ok t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_4boezR/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/43_vg_simplify.t .... 1..5 not ok 1 - vg simplify runs through when popping small bubbles # got: '132' # expected: '0' not ok 2 - simplification pops all the bubbles in a simple graph # got: '' # expected: '1' ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants not ok 5 - simplification keeps only some variants # got: '' # expected: '118' Failed 3/5 subtests t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_oFTehQ/stacktrace.txt Please include the stack trace file in your bug report! WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/45_vg_sort.t ........ 1..5 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing not ok 3 - a vg graph can be sorted topologically # got: '132' # expected: '0' ok 4 - a vg graph can be sorted with Eades algorithm without crashing ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing Failed 1/5 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ALdzqY/stacktrace.txt Please include the stack trace file in your bug report! warning: [vg index] providing input XG with option -x is deprecated t/46_vg_minimizer.t ... 1..14 ok 1 - default parameters ok 2 - single-threaded construction ok 3 - construction is deterministic ok 4 - syncmer index ok 5 - construction is deterministic ok 6 - minimizer parameters ok 7 - setting -k -w works correctly ok 8 - construction from GBWTGraph ok 9 - construction is deterministic ok 10 - construction with payload not ok 11 - construction is deterministic # got: '58b2bd98902df9acbe416bcfde649571' # expected: '58a6780c18921e4f6701b57fdb9c2e44' ok 12 - multiple graphs: first ok 13 - multiple graphs: second ok 14 - construction is deterministic Failed 1/14 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_1iXhsx/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open hla.xg while loading handlegraph::PathHandleGraph t/47_vg_dotplot.t ..... 1..1 not ok 1 - vg dotplot runs successfully # got: '1' # expected: '0' Failed 1/1 subtests warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_z6GrA0/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_zLjs61/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_KSLunb/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_ygd5ZM/stacktrace.txt Please include the stack trace file in your bug report! t/48_vg_convert.t: line 107: 1353041 Segmentation fault (core dumped) vg map -x zflat.vg -g zflat.gcsa -G sim.gam > sim-map.gam warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. warning [vg convert]: Converting a GFA to an indexed sequence graph from piped input can be memory intensive because the entire GFA must be loaded into memory. If memory usage is too high, consider serializing the GFA to disk to allow multiple passes over the file. t/48_vg_convert.t ..... 1..26 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout ODGI conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - odgi conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 14 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 15 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 17 - vg convert gam -> gaf -> gam preserves sequence ok 18 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 19 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 20 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads ok 21 - split alignment converted using deletions to represent internal offsets ok 22 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 23 - convert gam->gaf->gam on softclipped read preserves sequence ok 24 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 25 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_eU45io/stacktrace.txt Please include the stack trace file in your bug report! t/49_vg_depth.t ....... 1..4 not ok 1 - vg depth gets correct depth from gam # got: 'nan' # expected: '18' not ok 2 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from pack' not ok 3 - vg depth gets correct number of bins # got: '0' # expected: '5' not ok 4 - vg depth gets correct depth from gaf # got: 'nan' # expected: '18' Failed 4/4 subtests ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_iDIbpu/stacktrace.txt Please include the stack trace file in your bug report! index file x.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_QEh9UX/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_EvSyBm/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_0sF2rf/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_aJ6JYc/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_8SWFN0/stacktrace.txt Please include the stack trace file in your bug report! index file xy.fa.fai not found, generating... ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PA4gQX/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 4 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_hrZloh/stacktrace.txt Please include the stack trace file in your bug report! t/50_vg_giraffe.t ..... 1..20 ok 1 - a read can be mapped with all indexes specified without crashing ok 2 - a read can be mapped with syncmer indexes without crashing not ok 3 - a read can be mapped with just FASTA and VCF without crashing # got: '132' # expected: '0' not ok 4 - mapping with just a FASTA and a VCF produced JSON-able alignments # got: '1' # expected: '0' 1d0 < {"annotation": {"mapq_explored_cap": 57.653475280336039, "mapq_uncapped": 3, "secondary_scores": [63, 63]}, "identity": 0.96825396825396826, "mapping_quality": 3, "name": "read", "path": {"mapping": [{"edit": [{"from_length": 1, "sequence": "T", "to_length": 1}], "position": {"node_id": "96"}, "rank": "1"}, {"edit": [{"from_length": 2, "to_length": 2}], "position": {"node_id": "98"}, "rank": "2"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "100"}, "rank": "3"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"node_id": "101"}, "rank": "4"}, {"edit": [{"from_length": 26, "to_length": 26}], "position": {"node_id": "102"}, "rank": "5"}, {"edit": [{"from_length": 1, "sequence": "C", "to_length": 1}], "position": {"node_id": "104"}, "rank": "6"}]}, "quality": "QkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJCQkJC", "score": 63, "sequence": "TTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCC"} not ok 5 - mapping to manually-generated indexes and automatically-generated indexes is the same # got: '1' # expected: '0' ok 6 - mapping with syncmers produces the same alignment as mapping with minimizers not ok 7 - unpaired reads lack cross-references # got: '0' # expected: '1000' ok 8 - paired reads have cross-references not ok 9 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 10 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 11 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 12 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 13 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 14 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 15 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 16 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 17 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 18 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:y LN:1001 > @SQ SN:x LN:1001 not ok 19 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order # got: '1' # expected: '0' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:x LN:1001 > @SQ SN:y LN:1001 not ok 20 - surjecting with a sequence dictionary in sorted order produces headers in sorted order # got: '1' # expected: '0' Failed 16/20 subtests Test Summary Report ------------------- t/00_unittest.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/02_vg_construct.t (Wstat: 0 Tests: 28 Failed: 1) Failed test: 25 t/04_vg_align.t (Wstat: 0 Tests: 20 Failed: 20) Failed tests: 1-20 t/05_vg_find.t (Wstat: 0 Tests: 27 Failed: 2) Failed tests: 16-17 t/06_vg_index.t (Wstat: 0 Tests: 51 Failed: 2) Failed tests: 37, 49 t/07_vg_map.t (Wstat: 0 Tests: 54 Failed: 45) Failed tests: 1-14, 17-21, 24-31, 33, 38-54 t/08_vg_ids.t (Wstat: 0 Tests: 10 Failed: 6) Failed tests: 4-5, 7-10 t/10_vg_stats.t (Wstat: 0 Tests: 18 Failed: 2) Failed tests: 8, 10 t/11_vg_paths.t (Wstat: 0 Tests: 14 Failed: 1) Failed test: 12 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 16) Failed tests: 5-11, 14, 16, 18-21, 25, 29-30 t/15_vg_surject.t (Wstat: 0 Tests: 33 Failed: 28) Failed tests: 1-13, 16, 20-33 t/16_vg_msga.t (Wstat: 0 Tests: 14 Failed: 12) Failed tests: 1-4, 7-14 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 21) Failed tests: 11-19, 22-23, 26-27, 29-30, 32-33, 35-36 38-39 t/18_vg_call.t (Wstat: 0 Tests: 12 Failed: 4) Failed tests: 2, 4-5, 11 t/26_deconstruct.t (Wstat: 0 Tests: 19 Failed: 17) Failed tests: 1-5, 7-18 t/27_vg_genotype.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1-2, 5 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 8) Failed tests: 1-2, 4, 7-8, 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 9 Failed: 5) Failed tests: 1-4, 8 t/33_vg_mpmap.t (Wstat: 0 Tests: 17 Failed: 16) Failed tests: 1-12, 14-17 t/34_vg_pack.t (Wstat: 0 Tests: 18 Failed: 2) Failed tests: 1, 18 t/40_vg_gamcompare.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1, 3, 5 t/43_vg_simplify.t (Wstat: 0 Tests: 5 Failed: 3) Failed tests: 1-2, 5 t/45_vg_sort.t (Wstat: 0 Tests: 5 Failed: 1) Failed test: 3 t/46_vg_minimizer.t (Wstat: 0 Tests: 14 Failed: 1) Failed test: 11 t/47_vg_dotplot.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/49_vg_depth.t (Wstat: 0 Tests: 4 Failed: 4) Failed tests: 1-4 t/50_vg_giraffe.t (Wstat: 0 Tests: 20 Failed: 16) Failed tests: 3-5, 7, 9-20 Files=49, Tests=758, 19283 wallclock secs ( 0.63 usr 0.20 sys + 13806.59 cusr 1209.48 csys = 15016.90 CPU) Result: FAIL make[1]: *** [debian/rules:74: override_dh_auto_test-arch] Error 255 make[1]: Leaving directory '/build/vg-OlWF3C/vg-1.30.0+ds' make: *** [debian/rules:22: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 E: run_chroot failed: E: command failed: chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/vg-OlWF3C/vg-1.30.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504693" dpkg-buildpackage -uc -a amd64 --build=any" W: listening on child socket failed: I: removing tempdir /tmp/mmdebstrap.qHx75qFUFT... mmdebstrap failed